Re: [R] creating a variable using concatenation
On Mar 30, 2010, at 11:15 PM, Steve Chen wrote: You can try this: library(tutoR) That's an interesting set of goals: Package to mask common functions so that inputs in error are explained and able to be corrected, prior to execution. 'assist' offers step-by-step assistance to correctly call a function such as 'par'. 'eg' picks out Examples first and foremost in help. With 'deskcheck', execution is initiated and the 'debug' flag utilized, to help deskcheck a function. plot(eval.string(toplot)) Can't say as I learned very much about R by reading the code for eval.string, but the idea of having a learning-mode for R that would clue in the newbs among us when we committed common errors, rather than wrapping things up in a GUI, has a certain intriguing aspect to it. Is there a literature regarding how well such a strategy plays out in practice? -- David. Steve Chen On 2010/3/31 上午 09:24, zubin wrote: A general problem i run into, i know there must be a simple solution. I like to create a variable by appending a 1 for example, (i need to loop later on from 1 to X, thus the reason for this). So i assign the variable vplot with this value, however it has quotes and when i use it in a barplot, it throws an error. but the tcenter$X1 does exist, its an element of a data frame. So if i type directly it works, but i like to do this programmatically, as i have to generate a bunch of these plots and need to loop. So how do i concatenate to create a variable, then reference that variable in a function call? R x- data.frame(1,2,3,4,5,6,7,8) R x X1 X2 X3 X4 X5 X6 X7 X8 1 1 2 3 4 5 6 7 8 R x$X1 [1] 1 R i=1 R toplot- paste(x$X,i,sep=) R toplot [1] x$X1 okay lets test: R plot(x$X1) -it works i see the plot however this DOES not work R plot(toplot) Error in plot.window(...) : need finite 'ylim' values In addition: Warning messages: 1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion 2: In min(x) : no non-missing arguments to min; returning Inf 3: In max(x) : no non-missing arguments to max; returning -Inf Thus, that's my problem, i know it must be simple - the variable is equal to x$X1 but it does not work in a function call? i tried many functions - always some type of error. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Predict function in ARIMA/GARCH- Real time forecastinng
Hi, I m working on time series forecasting.I was checking ARIMA and GARCH model for forecasting.Is there any possibility that we can include test data as input for predict function.I am working on real time forecasting where i would be getting real time feeds using which i need forecast.As of now in Predict function we can use how many periods ahead we need the forecast.As of now we cannot use Predict function for real time forecasting.Is there any work around so that we can input the test data as one of the input to Predict function so that it can be used in real time scenarios? Regards, Raghav [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nlsList{nlme} control of min and max parameter bounds?
Steve Oswald wrote: I'm analysing growth rates using a gompertz (logistic) curve and am attempting to fit parameters for all of my study birds using nlsList. I've been looking for an option in nlsList to set min and max limits for parameter values during estimation, although I have failed to find any under 'control'. If you want to constrain to positive parameters only, as in pharmacology, fitting the logs of the parameters might help. For more general constraints, check the examples in optim. Dieter Hi All I'm analysing growth rates using a gompertz (logistic) curve and am attempting to fit parameters for all of my study birds using nlsList. I've been looking for an option in nlsList to set min and max limits for parameter values during estimation, although I have failed to find any under 'control'. Other users seem to have reported that using control in the port algorithm (as in an nls fit) failed to work and it didn't work in my case either. Is there such a control for nlsList? I did fashion a selfStart function with a work-around loop in it. This subsetted the data by ID and performed separate nls fits with parameters constrained by the port algorithm. My objective was to use nlsList as an object for an nlme fit, so I was thinking of pasting together the details of the fits from my slefStart function into an object of class nlsList lmList but wasn't sure if this would work or was even appropriate. Thanks for your help Steve Dr. Steve Oswald Penn State Berks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://n4.nabble.com/nlsList-nlme-control-of-min-and-max-parameter-bounds-tp1746242p1746347.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Install package of BRugs?
Hua Li wrote: I'm trying to install the package BRugs and could not find it on the install package list. Then I tried the suggestion to run the following command in R install.packages(BRugs) Use R2WinBUGS instead http://cran.at.r-project.org/web/packages/R2WinBUGS/index.html Dieter -- View this message in context: http://n4.nabble.com/Install-package-of-BRugs-tp1745751p1746351.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Install package of BRugs?
On 30.03.2010 22:01, David Winsemius wrote: On Mar 30, 2010, at 3:42 PM, Hua Li wrote: Hi All, I'm trying to install the package BRugs and could not find it on the install package list. Then I tried the suggestion to run the following command in R install.packages(BRugs) but get the following error message: Loading required package: BRugs Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'BRugs' and the command of library(BRugs) results in the following Error in library(BRugs) : there is no package called 'BRugs' So how can I install BRugs at this point? I'm using R 2.8.1 on Windows XP profession x64 edition. The glaringly obvious search strategy: r-project brugs on google provides this as the first hit: http://cran.r-project.org/web/packages/BRugs/ BRugs is hosted on CRAN extras (Brian Ripley's special cases repository) due to license specific issues. Please update your R and try install.packages(BRugs) again, you will get it from CRAN extras which is a default repository under Windows (unless you deselected it). Uwe Ligges Thanks a lot! Hua __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Install package of BRugs?
On 31.03.2010 08:36, Dieter Menne wrote: Hua Li wrote: I'm trying to install the package BRugs and could not find it on the install package list. Then I tried the suggestion to run the following command in R install.packages(BRugs) Use R2WinBUGS instead http://cran.at.r-project.org/web/packages/R2WinBUGS/index.html Dieter Dieter, thanks for the pointer, but I highly recommend *not* to use R2WinBUGS if you are under Windows but use BRugs which has a much cleaner interface and . It is hosted on CRAN extras (Brian Ripley's special cases repository) due to license specific issues. Please update your R and try install.packages(BRugs) again, you will get it from CRAN extras which is a default repository under Windows (unless you deselected it). Best wishes, Uwe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Install package of BRugs?
Uwe Ligges-3 wrote: Use R2WinBUGS instead Dieter, thanks for the pointer, but I highly recommend *not* to use R2WinBUGS if you are under Windows but use BRugs which has a much cleaner interface and . Ahem... yes. I am aware of this, and I had mixed things up! Dieter -- View this message in context: http://n4.nabble.com/Install-package-of-BRugs-tp1745751p1746371.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] decomposing the error term into time-specific indiviual specific effect + transitory term
hi all! i am a beginner in R so i need a command that i couldnt find on the net. i need to transform the error term and i should decompose it into time-specific, indiviual specific effect and transitory term like here (åit =ui + vt + wit) the individual effect in my model is called stno and time effect is called year, can somebody send me the command to decompose (without forgetting that i am a beginner)? Thank you very much! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] is and the story of a typo
On 30-Mar-10 23:23:09, Jim Lemon wrote: Hi all, The gurus may pour scorn on me for not knowing this, but I happened to mistype if as is in the heat of debugging a function. As I scanned the debugged function with some satisfaction, I noticed the error. How could this have worked? I assume that is is a generic function that calls one of the is.* functions to evaluate whatever is passed. It appears that this particular typo causes is to work out and report the contents of its argument. Ho hum. As I did not test the FALSE result, I never would have noticed that it was not the conditional statement I expected until it evaluated something that should have been FALSE. Jim Hi Jim, is: ?is is(is) is(is(is)) is(is(is(is))) identical(is(is(is)),is(is(is(is Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 31-Mar-10 Time: 09:21:29 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] MySQL and RODBC - limitations
Thanks guys - that is better. You all rock! -- View this message in context: http://n4.nabble.com/MySQL-and-RODBC-limitations-tp1692743p1746457.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Weird R behaviour?
Dear list, I have observed a weird behaviour from R --- apologies if I am missing something obvious! df3f826f28 df3f826f28 Say you type in R: c.preec - 10074 c.gd - 2200 p1 - .2 c.neo - p1*9451 + (1-p1)*3883 n.preec - 3710 n.gd - 2650 n.neo - 2120 n.pcos - 53000 unit.met - 94 cost.met - 94*n.pcos effect - seq(0,1,.01) gross.save - ((n.preec*effect*c.preec) + (n.gd*effect*c.gd) + (n.neo*effect*c.neo)) save.nhs - gross.save - cost.met e.star - .4 s.star - save.nhs[which(effect==e.star)]/100 Now, R should return which(effect==e.star) = 41 and therefore compute the variable s.star. All well and trivial; but if you try and set e.star - .7 R returns which(effect==e.star) = integer(0) so apparently there is no element in the vector e.star that is equal to .7. Of course, there should be, since effect - seq(0,1,.01), and in fact if you ask R to show you the vector effect, you do get [1] 0.00 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.10 0.11 0.12 0.13 0.14 [16] 0.15 0.16 0.17 0.18 0.19 0.20 0.21 0.22 0.23 0.24 0.25 0.26 0.27 0.28 0.29 [31] 0.30 0.31 0.32 0.33 0.34 0.35 0.36 0.37 0.38 0.39 0.40 0.41 0.42 0.43 0.44 [46] 0.45 0.46 0.47 0.48 0.49 0.50 0.51 0.52 0.53 0.54 0.55 0.56 0.57 0.58 0.59 [61] 0.60 0.61 0.62 0.63 0.64 0.65 0.66 0.67 0.68 0.69 *0.70* 0.71 0.72 0.73 0.74 [76] 0.75 0.76 0.77 0.78 0.79 0.80 0.81 0.82 0.83 0.84 0.85 0.86 0.87 0.88 0.89 [91] 0.90 0.91 0.92 0.93 0.94 0.95 0.96 0.97 0.98 0.99 1.00 Can anyone think of why this happens? Many thanks Gianluca [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Weird R behaviour?
FAQ 7.31: Why doesn't R think these numbers are equal? http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f b On Wed, Mar 31, 2010 at 10:10 AM, Gianluca Baio gianl...@statistica.it wrote: Dear list, I have observed a weird behaviour from R --- apologies if I am missing something obvious! df3f826f28 df3f826f28 Say you type in R: c.preec - 10074 c.gd - 2200 p1 - .2 c.neo - p1*9451 + (1-p1)*3883 n.preec - 3710 n.gd - 2650 n.neo - 2120 n.pcos - 53000 unit.met - 94 cost.met - 94*n.pcos effect - seq(0,1,.01) gross.save - ((n.preec*effect*c.preec) + (n.gd*effect*c.gd) + (n.neo*effect*c.neo)) save.nhs - gross.save - cost.met e.star - .4 s.star - save.nhs[which(effect==e.star)]/100 Now, R should return which(effect==e.star) = 41 and therefore compute the variable s.star. All well and trivial; but if you try and set e.star - .7 R returns which(effect==e.star) = integer(0) so apparently there is no element in the vector e.star that is equal to .7. Of course, there should be, since effect - seq(0,1,.01), and in fact if you ask R to show you the vector effect, you do get [1] 0.00 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.10 0.11 0.12 0.13 0.14 [16] 0.15 0.16 0.17 0.18 0.19 0.20 0.21 0.22 0.23 0.24 0.25 0.26 0.27 0.28 0.29 [31] 0.30 0.31 0.32 0.33 0.34 0.35 0.36 0.37 0.38 0.39 0.40 0.41 0.42 0.43 0.44 [46] 0.45 0.46 0.47 0.48 0.49 0.50 0.51 0.52 0.53 0.54 0.55 0.56 0.57 0.58 0.59 [61] 0.60 0.61 0.62 0.63 0.64 0.65 0.66 0.67 0.68 0.69 *0.70* 0.71 0.72 0.73 0.74 [76] 0.75 0.76 0.77 0.78 0.79 0.80 0.81 0.82 0.83 0.84 0.85 0.86 0.87 0.88 0.89 [91] 0.90 0.91 0.92 0.93 0.94 0.95 0.96 0.97 0.98 0.99 1.00 Can anyone think of why this happens? Many thanks Gianluca [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Create a new variable
Hi
r-help-boun...@r-project.org napsal dne 30.03.2010 18:46:35:
Hello,
Thomas Jensen wrote:
Dear R-list,
Sorry for spamming the list lately, I am just learning the more
advanced
aspects of R!
I have some data that looks like this:
Out Country1 Country 2 Country 3 ... CountryN
1 1 1 1 1
0 1 1 0 1
1 1 0 1 0
Don't paste data like this to the list. Use ?dput to create an easy to
use data.frame that users of the list can input with one R command. You
will most likely get help very quickly at that point since our data will
match your's exactly.
I want to create a new variable that counts the number of zeros in
every
row whenever Out is equal to 1, and else it is a zero, so it would
look
like this:
new_var
0
0
2
I have tried the following:
for (i in length(Out)){
if (Out == 1) {new_var - sum(dat[i,] != 1)}
else {new_var - 0}
}
but this gives me an error message.
I have not tested any of this, but I'm guessing something like the
following would work. Assume your data.frame is called df.
#NOT TESTED
tmp - apply(df, 1, function(x) sum(x == 0))
df$new_var - ifelse(df$Out == 1, tmp, 0)
Maybe this can work too
df$new_var - rowSums(df[, -1] ==0) * (df$Out==1)
Regards
Petr
See ?apply and ?ifelse .
Best, Thomas
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[R] Odp: (no subject)
Hi r-help-boun...@r-project.org napsal dne 31.03.2010 06:15:38: Hi r-users, I would like to display my legend with fill box and line symbol. The first color will be in the box and the second colour will just be a line. legend(topright, c(observed,gamma sum fit), col= c (greenyellow,red),pch=c(15, NA),lty = c(0,1),lwd=2) Is it possible? Did you try it? Regards Petr Thank you. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Truncated Distributions - Estimating parameters
Dear R users, I am working on the Value at Risk (VaR) for the Operational risk. For a given loss data, we try to fit some statistical distributions using Kolmogorov-Smirnov (KS) test and A-D test and then for fitted distribution using the estimated parameters, the losses are simulated and the VaR is arrived at. The typical problem faced by the banks is the paucity of Internal loss data and thus banks depend on the external loss data obtained from external sources. This external data is normally of higher magnitude than the internal loss data of the bank. Thus using regression technique, this external data is scaled and then the internal data and the scaled external data is combined. Then we try to fit some statistical distribution to this combined data. However, at times it becomes very difficult to fit any distribution to this particular combined data as the data becomes Bimodal. The paper by G. Dionne and Hela Dahen What about underevaluating Operational Value at Risk in the Banking sector? suggests that we fit two distributions (1) to the internal data (called body part) with Upper cap or upper bound to the loss data and (2) to the external data with Lower bound (called Tail part). Thus, now I am dealing with two truncated distributions (i) having a lower loss bound (say 5000$ i.e. bank records only those losses exceeding 5,000$) and having an Upper bound of say 500,000$; and (ii) having lower loss bound of say 500,000$ and no upper limit. My question is (1) Is there any R package which helps to estimate the parameters of various Truncated distributions? (2) How to fit the truncated distributions to loss data in the sense how do we use KS and AD tests? Extremely sorry for writing such a long mail. Regards Julia Only a man of Worth sees Worth in other men [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] (no subject)
On 03/31/2010 03:15 PM, Roslina Zakaria wrote: Hi r-users, I would like to display my legend with fill box and line symbol. The first color will be in the box and the second colour will just be a line. legend(topright, c(observed,gamma sum fit), col= c(greenyellow,red),pch=c(15, NA),lty = c(0,1),lwd=2) Hi Rosalina, I think what you're trying to do requires the argument: pt.cex=2 in the call to legend Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Simplifying particular piece of code
Hello, everyone
I have a piece of code that looks like this:
mrets - merge(mrets, BMM.SR=apply(mrets, 1, MyFunc, ret=BMM.AV120,
stdev=BMM.SD120))
mrets - merge(mrets, GM1.SR=apply(mrets, 1, MyFunc, ret=GM1.AV120,
stdev=GM1.SD120))
mrets - merge(mrets, IYC.SR=apply(mrets, 1, MyFunc, ret=IYC.AV120,
stdev=IYC.SD120))
mrets - merge(mrets, FCA.SR=apply(mrets, 1, MyFunc, ret=FCA.AV120,
stdev=FCA.SD120))
mrets - merge(mrets, IMM.SR=apply(mrets, 1, MyFunc, ret=IMM.AV120,
stdev=IMM.SD120))
mrets - merge(mrets, BME.SR=apply(mrets, 1, MyFunc, ret=BME.AV120,
stdev=BME.SD120))
mrets - merge(mrets, CRT.SR=apply(mrets, 1, MyFunc, ret=CRT.AV120,
stdev=CRT.SD120))
mrets - merge(mrets, GTF.SR=apply(mrets, 1, MyFunc, ret=GTF.AV120,
stdev=GTF.SD120))
mrets - merge(mrets, ERU.SR=apply(mrets, 1, MyFunc, ret=ERU.AV120,
stdev=ERU.SD120))
mrets - merge(mrets, ERE.SR=apply(mrets, 1, MyFunc, ret=ERE.AV120,
stdev=ERE.SD120))
mrets - merge(mrets, EPT.SR=apply(mrets, 1, MyFunc, ret=EPT.AV120,
stdev=EPT.SD120))
mrets - merge(mrets, EVA.SR=apply(mrets, 1, MyFunc, ret=EVA.AV120,
stdev=EVA.SD120))
mrets - merge(mrets, EMT.SR=apply(mrets, 1, MyFunc, ret=EMT.AV120,
stdev=EMT.SD120))
mrets - merge(mrets, EMM.SR=apply(mrets, 1, MyFunc, ret=EMM.AV120,
stdev=EMM.SD120))
mrets - merge(mrets, EMV.SR=apply(mrets, 1, MyFunc, ret=EMV.AV120,
stdev=EMV.SD120))
mrets - merge(mrets, ETM.SR=apply(mrets, 1, MyFunc, ret=ETM.AV120,
stdev=ETM.SD120))
Is there a way to simplify this, some sort of loop?
mrets is a zoo object.
.AV120 and .SD120 are columns in this object.
I need the exact .SR column names.
This does not work:
SRnames - paste(colnames.mrets, .SR, sep=)
AVnames - paste(colnames.mrets, .AV120, sep=)
SDnames - paste(colnames.mrets, .SD120, sep=)
for(i in seq(SRnames)){
mrets - merge(mrets, SRnames[i]=apply(mrets, 1, MyFunc,
ret=AVnames[i], stdev=SDnames[i]))
}
Help much appreciated.
Regards,
Sergey
--
Simplicity is the last step of art./Bruce Lee
The more you know, the more you know you don't know. /Myself
I'm not young enough to know everything. /Oscar Wilde
Experience is one thing you can't get for nothing. /Oscar Wilde
When you are finished changing, you're finished. /Benjamin Franklin
Luck is where preparation meets opportunity. /George Patten
Kniven skärpes bara mot stenen.
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Re: [R] Simplifying particular piece of code
How about this (not tested, since you did not provide example data nor
function code):
---
SRnames - paste(colnames.mrets, .SR, sep=)
AVnames - paste(colnames.mrets, .AV120, sep=)
SDnames - paste(colnames.mrets, .SD120, sep=)
names.matrix-cbind(SRnames,AVnames,SDnames)
mrets.list-apply(names.matrix,1,function(.names){
apply(mrets,1,MyFunc,ret=.names[2],stdev=.names[3]}
)
names(mrets.list)-names.matrix[,1]
mrets-do.call(merge,mrets.list)
-
?
/Gustaf
On Wed, Mar 31, 2010 at 12:10 PM, Sergey Goriatchev serg...@gmail.com wrote:
Hello, everyone
I have a piece of code that looks like this:
mrets - merge(mrets, BMM.SR=apply(mrets, 1, MyFunc, ret=BMM.AV120,
stdev=BMM.SD120))
mrets - merge(mrets, GM1.SR=apply(mrets, 1, MyFunc, ret=GM1.AV120,
stdev=GM1.SD120))
mrets - merge(mrets, IYC.SR=apply(mrets, 1, MyFunc, ret=IYC.AV120,
stdev=IYC.SD120))
mrets - merge(mrets, FCA.SR=apply(mrets, 1, MyFunc, ret=FCA.AV120,
stdev=FCA.SD120))
mrets - merge(mrets, IMM.SR=apply(mrets, 1, MyFunc, ret=IMM.AV120,
stdev=IMM.SD120))
mrets - merge(mrets, BME.SR=apply(mrets, 1, MyFunc, ret=BME.AV120,
stdev=BME.SD120))
mrets - merge(mrets, CRT.SR=apply(mrets, 1, MyFunc, ret=CRT.AV120,
stdev=CRT.SD120))
mrets - merge(mrets, GTF.SR=apply(mrets, 1, MyFunc, ret=GTF.AV120,
stdev=GTF.SD120))
mrets - merge(mrets, ERU.SR=apply(mrets, 1, MyFunc, ret=ERU.AV120,
stdev=ERU.SD120))
mrets - merge(mrets, ERE.SR=apply(mrets, 1, MyFunc, ret=ERE.AV120,
stdev=ERE.SD120))
mrets - merge(mrets, EPT.SR=apply(mrets, 1, MyFunc, ret=EPT.AV120,
stdev=EPT.SD120))
mrets - merge(mrets, EVA.SR=apply(mrets, 1, MyFunc, ret=EVA.AV120,
stdev=EVA.SD120))
mrets - merge(mrets, EMT.SR=apply(mrets, 1, MyFunc, ret=EMT.AV120,
stdev=EMT.SD120))
mrets - merge(mrets, EMM.SR=apply(mrets, 1, MyFunc, ret=EMM.AV120,
stdev=EMM.SD120))
mrets - merge(mrets, EMV.SR=apply(mrets, 1, MyFunc, ret=EMV.AV120,
stdev=EMV.SD120))
mrets - merge(mrets, ETM.SR=apply(mrets, 1, MyFunc, ret=ETM.AV120,
stdev=ETM.SD120))
Is there a way to simplify this, some sort of loop?
mrets is a zoo object.
.AV120 and .SD120 are columns in this object.
I need the exact .SR column names.
This does not work:
SRnames - paste(colnames.mrets, .SR, sep=)
AVnames - paste(colnames.mrets, .AV120, sep=)
SDnames - paste(colnames.mrets, .SD120, sep=)
for(i in seq(SRnames)){
mrets - merge(mrets, SRnames[i]=apply(mrets, 1, MyFunc,
ret=AVnames[i], stdev=SDnames[i]))
}
Help much appreciated.
Regards,
Sergey
--
Simplicity is the last step of art./Bruce Lee
The more you know, the more you know you don't know. /Myself
I'm not young enough to know everything. /Oscar Wilde
Experience is one thing you can't get for nothing. /Oscar Wilde
When you are finished changing, you're finished. /Benjamin Franklin
Luck is where preparation meets opportunity. /George Patten
Kniven skärpes bara mot stenen.
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--
Gustaf Rydevik, M.Sci.
tel: +46(0)703 051 451
address:Essingetorget 40,112 66 Stockholm, SE
skype:gustaf_rydevik
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[R] time series datasets
Hello, I am searching large multivariate time series datasets to use with R. Can any one help me??? Regards, Vibha [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Generative Topographic Map
I tried to use R version of package
I noticed the original MatLab Pckage is much better documented.
I had a look at the R demo code gtm_demo and found that variable Y is used in
advanced of being created:
I wrote my own few lines as follows:
inDir - C:/Documents and Settings/Monville/Alanine Dipeptide/DBP1/DHA
setwd(inDir)
T - read.table(DHA_TNH.txt)
L - 3
X - matrix(nrow=nrow(T),ncol=3,byrow=TRUE)
MU - matrix(nrow=round(nrow(T)/5), ncol=L)
for(i in 1:ncol(X)) {
for(j in 1:nrow(X)) {
X[j,i] - RANDU()
}
}
for(i in 1:ncol(MU)) {
for(j in 1:nrow(MU)) {
MU[j,i] - RANDU()
}
}
sigma -1
FI - gtm_gbf(MU,sigma,X)
W - gtm_ri(T,FI)
Y= FI%*%W
b = gtm_bi(Y)
lambda - 0.001
for (m in 1:15) {
trnResult = gtm_trn(T, FI, W, lambda, 1, b, 2,quiet = TRUE, minSing = 0.01)
W = trnResult$W
b = trnResult$beta
Y = FI %*% W
}
I ran the above script on my own data representing 1969 samples of 7 dihedral
angles of a folding molecule (attached.
Upon running the 1st iteration of the training function gtm_trn I get the
following error that I cannot interpret.
Any help and/or suggestion is welcome:
trnResult = gtm_trn(T, FI, W, lambda, 1, b, 2,quiet = TRUE, minSing = 1.)
Error in gtmGlobalR %*% T :
requires numeric/complex matrix/vector arguments
In addition: Warning messages:
1: In chol.default(A, pivot = TRUE) : matrix not positive definite
2: In gtm_trn(T, FI, W, lambda, 1, b, 2, quiet = TRUE, minSing = 1) :
Using 7 out of 395 eigenvalues
Thank you in advance,
Maura
e tutti i telefonini TIM!
Vai su
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Re: [R] Value-at-Risk Portfolio(both equity and option)
Thank you very much. It is very helpful. As far as I understand, not easy to have a function to combine both the equity part and the option part? -- View this message in context: http://n4.nabble.com/Value-at-Risk-Portfolio-both-equity-and-option-tp1745179p1746520.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Error singular gradient matrix at initial parameter estimates in nls
If you have a perfect fit, you have zero residuals. But in the nls manual page we have: Warning: *Do not use ‘nls’ on artificial zero-residual data.* So this is a case of complaining that your diesel car is broken because you ignored the Diesel fuel only sign on the filler cap and put in gasoline. However I've not been happy with this choice in the code of nls -- it's been there a long time -- and my own codes from 1974 onwards have always handled zero residual cases. I do believe that the code could at least give a better diagnostic message. Zero residuals -- perfect fits -- arise when one is interested more or less in an interpolating function rather than doing statistics, and I can understand the reluctance of statisticians to countenance such a use of nls. And Bert's comment on overparametrization is almost certainly valid also. JN __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] interpretation of p values for highly correlated logistic analysis
Dear list, I want to perform a logistic regression analysis with multiple categorical predictors (i.e., a logit) on some data where there is a very definite relationship between one predicator and the response/independent variable. The problem I have is that in such a case the p value goes very high (while I as a naive newbie would expect it to crash towards 0). I'll illustrate my problem with some toy data. Say I have the following data as an input frame: roman animal colour 1 alphadog black 2 betacat white 3 alphadog black 4 alphacat black 5 betadog white 6 alphacat black 7 gammadog white 8 alphacat black 9 gammadog white 10 betacat white 11 alphadog black 12 alphacat black 13 gammadog white 14 alphacat black 15 betadog white 16 betacat black 17 alphacat black 18 betadog white In this toy data you can see that roman:alpha and roman:beta are pretty good predictors of colour Let's say I perform logistic analysis directly on the raw data with colour as a response variable: options(contrasts=c(contr.treatment,contr.poly)) anal1 - glm(data$colour~data$roman+data$animal,family=binomial) then I find that my P values for each individual level coefficient approach 1: Coefficients: Estimate Std. Error z value Pr(|z|) (Intercept) -41.65 19609.49 -0.0020.998 data$romanbeta 42.35 19609.49 0.0020.998 data$romangamma43.74 31089.48 0.0010.999 data$animaldog 20.48 13866.00 0.0010.999 while I expect the p value for roman:beta to be quite low because it is a good predictor of colour:white On the other hand, if I then run an anova with a Chi-sq test on the result model, I find as I would expect that 'roman' is a good predictor of colour. anova(anal1,test=Chisq) Analysis of Deviance Table Model: binomial, link: logit Response: data$colour Terms added sequentially (first to last) Df Deviance Resid. Df Resid. Dev P(|Chi|) NULL 1724.7306 data$roman 2 19.323915 5.4067 6.366e-05 *** data$animal 1 1.587614 3.81910.2077 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Can anyone please explain why my p value is so high for the individual levels? Sorry for what is likely a stupid question. Claus p.s., when I run logistic analysis on data that is more 'randomised' everything comes out as I expect. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] RCOM Save
Dear all, I use the package RCOM to manipulate Excel-Files (Windows). After opening the Excel-File and formatting the cells I want to save the file automatically without request. If I use y[[Save]] - TRUE it opens the saving dialog and I have to select the destination for saving. But I simply want to overwrite the existing file without any other workings. Thany your very much in advance. Jens. -- View this message in context: http://n4.nabble.com/RCOM-Save-tp1746602p1746602.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RCOM Save
Try adding this: y[[DisplayAlerts]] - FALSE On Wed, Mar 31, 2010 at 8:28 AM, koj jens.k...@gmx.li wrote: Dear all, I use the package RCOM to manipulate Excel-Files (Windows). After opening the Excel-File and formatting the cells I want to save the file automatically without request. If I use y[[Save]] - TRUE it opens the saving dialog and I have to select the destination for saving. But I simply want to overwrite the existing file without any other workings. Thany your very much in advance. Jens. -- View this message in context: http://n4.nabble.com/RCOM-Save-tp1746602p1746602.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ggplot2: Adding points to a density plot
Hi, Consider something like library(ggplot2) movies$decade - round_any(movies$year, 10) m - qplot(rating,data=movies,colour=factor(decade),geom=density) m (modified from ?stat_density). I'd like to add on the line y=0 a dot for the median of each decade category (using the same colour coding as the fill). I'm failing miserably at all my m + geom_point based approaches and would appreciate if someone could show me the ggplot2 way of achieving this. Thanks, Joh __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] interpretation of p values for highly correlated lo gistic analysis
claus orourke claus.orourke at gmail.com writes: look up Hauck-Donner effect ... __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Printing the function t.test() in R
Dear R Users, I have a question, how does one print an r function like t.test in R (to get the whole function and not just a summary of the environment)? For example if I type the following: t.test function (x, ...) UseMethod(t.test) environment: namespace:stats print(t.test) function (x, ...) UseMethod(t.test) environment: namespace:stats I don't get the entire function printed. Kind regards, -- Luwis Diya, Leuven Biostatistics and Statistical Bioinformatics Centre (L-BioStat), Kapucijnenvoer 35 blok d - bus 7001, 3000 Leuven, Belgium Tel: +32 16 336886 or +32 16 336892 Fax: +32 16 337015 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Value-at-Risk Portfolio(both equity and option)
One thing that comes to mind immediately is the 'blotter' package which I believe is designed to handle and track multiple instruments. A sloppy temporary solution I guess would be to do some type of lookup or a flag that denotes which instrument is an option and apply the VaR methodology appropriately. I am not in front of my desktop for now, else I would dig around the blotter code to evaluate a proposal to handle the scenario you mention. Perhaps some people who have done more work with these types of issues can shed more light on this. Hth -c On 3/31/10, zhang yn19...@msn.com wrote: Thank you very much. It is very helpful. As far as I understand, not easy to have a function to combine both the equity part and the option part? -- View this message in context: http://n4.nabble.com/Value-at-Risk-Portfolio-both-equity-and-option-tp1745179p1746520.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Sent from my mobile device __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Printing the function t.test() in R
Hi Luwis, this task is solved in the R Help Desk, see R News 6/4 http://cran.r-project.org/doc/Rnews/Rnews_2006-4.pdf in short t.test is a S3-method and you can have a look at implemented methods with methods(t.test) and then use e.g. getAnywhere(t.test.default) hth. Luwis Tapiwa Diya schrieb: Dear R Users, I have a question, how does one print an r function like t.test in R (to get the whole function and not just a summary of the environment)? For example if I type the following: t.test function (x, ...) UseMethod(t.test) environment: namespace:stats print(t.test) function (x, ...) UseMethod(t.test) environment: namespace:stats I don't get the entire function printed. Kind regards, -- Eik Vettorazzi Institut für Medizinische Biometrie und Epidemiologie Universitätsklinikum Hamburg-Eppendorf Martinistr. 52 20246 Hamburg T ++49/40/7410-58243 F ++49/40/7410-57790 -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf Körperschaft des öffentlichen Rechts Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Jörg F. Debatin (Vorsitzender) Dr. Alexander Kirstein Joachim Prölß Prof. Dr. Dr. Uwe Koch-Gromus __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] time series datasets
What kind of time series data? Finance? Econometrics? The 'quantmod' package allows for downloading of stock and FRED data online for analysis. I believe PerformanceAnalytics also has some datasets as well. -c On 3/31/10, vibha patel vibhapatel...@gmail.com wrote: Hello, I am searching large multivariate time series datasets to use with R. Can any one help me??? Regards, Vibha [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Sent from my mobile device __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Printing the function t.test() in R
On Mar 31, 2010, at 8:35 AM, Luwis Tapiwa Diya wrote: Dear R Users, I have a question, how does one print an r function like t.test in R (to get the whole function and not just a summary of the environment)? For example if I type the following: t.test function (x, ...) UseMethod(t.test) environment: namespace:stats print(t.test) function (x, ...) UseMethod(t.test) environment: namespace:stats I don't get the entire function printed. methods(t.test) [1] t.test.default* t.test.formula* Non-visible functions are asterisked # Noting the asterisk, one need to use getAnywhere() getAnywhere(t.test.default) A single object matching ‘t.test.default’ was found It was found in the following places registered S3 method for t.test from namespace stats namespace:stats with value function (x, y = NULL, alternative = c(two.sided, less, greater), mu = 0, paired = FALSE, var.equal = FALSE, conf.level = 0.95, ...) ### snipped the code - There was an R-News a couple of years back by (if memory serves) Ligges describing various methods for getting at source. Yes, there it is: Ligges, U. (2006): R Help Desk: Accessing the Sources. R News 6 (4), 43-45. http://cran.r-project.org/doc/Rnews/Rnews_2006-4.pdf -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem comparing hazard ratios
Thank you, gentlemen. I greatly appreciate your help. -- Michal J. Figurski, PhD HUP, Pathology Laboratory Medicine Biomarker Research Laboratory 3400 Spruce St. 7 Maloney Philadelphia, PA 19104 tel. (215) 662-3413 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] position of mismatches in all.equal()?
Dear R users, I would like to compare two dataframes, actually their categorical variables (as factors) only (there are 12, from column 1 to 12). The reason I do that is that I got 2 datasets from two different methods and I would like to be sure that each method used the same data (3D images) to extract 2 different sets of 3D parameters. Is it clear so far? So I thought about using all.equal() like this: test1 - data.frame(num=1:10, let1=letters[1:10], let2=letters[1:10]) test2 - data.frame(num=1:10, let1=letters[1:10], let2=letters[c(1:6, 6, 8:10)]) Since I want to compare only some columns, I do this: all.equal(test1[,1:2], test2[,1:2]) [1] TRUE all.equal(test1[,1:3], test2[,1:3]) [1] Component 3: Attributes: Component 2: Lengths (10, 9) differ (string compare on first 9) [2] Component 3: Attributes: Component 2: 3 string mismatches [3] Component 3: 1 string mismatch If I get TRUE, then everythin's fine. But if not, I just know from the output in which column(s) are the mismatches and how many (here 1). But my datasets are 2000+ rows, and I would like to know the row number(s) where mismatches occur. How can I do that? Thank you for your help! Regards, Ivan -- Ivan CALANDRA PhD Student University of Hamburg Biozentrum Grindel und Zoologisches Museum Abt. Säugetiere Martin-Luther-King-Platz 3 D-20146 Hamburg, GERMANY +49(0)40 42838 6231 ivan.calan...@uni-hamburg.de ** http://www.for771.uni-bonn.de http://webapp5.rrz.uni-hamburg.de/mammals/eng/mitarbeiter.php __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error singular gradient matrix at initial parameter estimates in nls
Dear JN, Bert, 1) It is not a perfect fit. I do not think I have ever said that. I said that an external algorithms fits the model without any problems: with ~ 500,000 data points and 19 paramters (ki in the original equation), it fits the model in less than 1 second. The data are not artificial data. The variables are independent (pi in the original model). The solution is unique and the rapidity of convergence is practically independent from the selection of start conditions (with a reasonable selection of start conditions at least). The resulting residuals are approximately normally distributed with mean 0 and sd ~ 4.23. 2) I agree with the comment of Bert on over-parametrization, but again the model is not overparamterised, and it is identifiable (in part answered already in (1)) Regards Prof. John C Nash wrote: If you have a perfect fit, you have zero residuals. But in the nls manual page we have: Warning: *Do not use ‘nls’ on artificial zero-residual data.* So this is a case of complaining that your diesel car is broken because you ignored the Diesel fuel only sign on the filler cap and put in gasoline. However I've not been happy with this choice in the code of nls -- it's been there a long time -- and my own codes from 1974 onwards have always handled zero residual cases. I do believe that the code could at least give a better diagnostic message. Zero residuals -- perfect fits -- arise when one is interested more or less in an interpolating function rather than doing statistics, and I can understand the reluctance of statisticians to countenance such a use of nls. And Bert's comment on overparametrization is almost certainly valid also. JN -- Corrado Topi PhD Researcher Global Climate Change and Biodiversity Area 18,Department of Biology University of York, York, YO10 5YW, UK Phone: + 44 (0) 1904 328645, E-mail: ct...@york.ac.uk __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ggplot2: Adding points to a density plot
Hi: Try this: library(ggplot2) movmed - ddply(movies, .(decade), summarise, med = median(rating)) m + geom_point(data = movmed, aes(x = med), y = 0, size = 2) HTH, Dennis On Wed, Mar 31, 2010 at 4:46 AM, Johannes Graumann johannes_graum...@web.de wrote: Hi, Consider something like library(ggplot2) movies$decade - round_any(movies$year, 10) m - qplot(rating,data=movies,colour=factor(decade),geom=density) m (modified from ?stat_density). I'd like to add on the line y=0 a dot for the median of each decade category (using the same colour coding as the fill). I'm failing miserably at all my m + geom_point based approaches and would appreciate if someone could show me the ggplot2 way of achieving this. Thanks, Joh __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] regular expression help to extract specific strings from text
Dear all,
Lets say I have the following:
x - c(Eve: Going to try something new today..., Adam: Hey @Eve, how are
you finding R? #rstats, Eve: @Adam, It's awesome, so much better at
statistics that #Excel ever was! @Cain @Able disagree though :(, Adam:
@Eve I'm sure they'll sort it out :), blahblah)
x
[1] Eve: Going to try something new
today...
[2] Adam: Hey @Eve, how are you finding R?
#rstats
[3] Eve: @Adam, It's awesome, so much better at statistics that
\n#Excel ever was! @Cain @Able disagree though :(
[4] Adam: @Eve I'm sure they'll sort it
out :)
[5] blahblah
I would like to come up with a data frame which looks like this
(pulling out the usernames and #tags):
data.frame(Msg = x, Source = c(Eve, Adam, Eve, Adam, NA), Mentions =
c(NA, Eve, Adam, Cain, Able, Eve, NA), HashTags = c(NA, rstats,
Excel, NA, NA))
The best I can do so far is:
source - lapply(x, function (x) {
tmp - strsplit(x, :, fixed = TRUE)
if(length(tmp[[1]]) 2) {
tmp - c(NA, tmp)
}
return(tmp[[1]][1])
} )
source - unlist(source)
[1] Eve Adam Eve Adam NA
I can't work out how to extract the usernames starting with '@' or the
#tags. I can identify them using gsub and replace them, but I don't
know how to just extract those terms only, e.g. sort of the opposite
of the following
gsub(@([A-Za-z0-9_]+), @[...], x)
[1] Eve: Going to try something new today...
[2] Adam: Hey @[...], how are you finding R? #rstats
[3] Eve: @[...], It's awesome, so much better at statistics that
#Excel ever was! @[...] @[...] disagree though :(
[4] Adam: @[...] I'm sure they'll sort it out :)
[5] blahblah
and
gsub(#([A-Za-z0-9_]+), #[...], x)
[1] Eve: Going to try something new today...
[2] Adam: Hey @Eve, how are you finding R? #[...]
[3] Eve: @Adam, It's awesome, so much better at statistics that
#[...] ever was! @Cain @Able disagree though :(
[4] Adam: @Eve I'm sure they'll sort it out :)
[5] blahblah
I hope that makes sense, and thank you kindly in advance for your
time.
Tony Breyal
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Re: [R] for loop; lm() regressions; list of vectors - lapply - accolades and square brackets??
Hello and thank you both for your answers! Dennis, I tried to simply run lm(a ~ b) after re-importing a as a matrix, but I get the following error message: Error in model.frame.default(formula = a ~ b, drop.unused.levels = TRUE) : invalid type (list) for variable 'a' so maybe I have to specify something in the arguments? What do you think? David, I tried your syntax as well, and received quasi-the same error statement: for(i in seq_along(a)) print(r - lm(a[i] ~ b) ) Error in model.frame.default(formula = a[i] ~ b, drop.unused.levels = TRUE) : invalid type (list) for variable 'a[i]' I am not too familiar with the use of accolades, square brackets and parentheses, the order in which they have to come in the function and the role they play, but I think they might be important... I also tried to use lapply; it works wonderfully for a basic function like: lapply(a, mean) I get a list of results with names and values..perfect! But with the lm() function... I just don't know how to write the arguments... tried several options without success... Any idea that could help me solve this only seemingly easy task would be most welcome!! Many Thanks, Driss Agramelal 2010/3/30 David Winsemius dwinsem...@comcast.net On Mar 30, 2010, at 12:42 PM, Driss Agramelal wrote: ## Hello everyone, ## ## I am trying to execute 150 times a lm regression using the 'for' loop, with 150 vectors for y, ## ## and always the same vector for x. ## ## I have an object with 150 elements named a, ## ## and a vector of 60 values named b. ## ## Each element in a has 60 values plus a header. ## ## When I type: r - lm(i ~ b) for(i in a) print(r) Try instead something like this untested modification: for(i in seq_along(a)) print(r - lm(a[i] ~ b) ) ## I get 150 times the lm results of the first element of a regressed with b, ## ## whereas I would like to have 150 different regression results from each element in a... ## ## Can someone please help me with the syntax of my loop please? ## ## Many Thanks, ## ## Driss Agramelal ## ## Switzerland ## [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT Hi: Did you try lm(a ~ b) ? According to the lm() help page, if a is a matrix, lm will regress each column of the matrix on the right hand side of the formula. Sounds like what you want... HTH, Dennis [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Installing JGR and rJava
Hello, I am running: R version 2.10.0 (2009-10-26) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 on a 64-bit RedHat box. To encourage collegues to use R, I am trying to install JGR, which depends on rJava, on the above machine. At first I received and error saying Java was not available. My IT support, I am not admin. on this machine, installed Java (1.6.0_19) and JDK (1.6.0_19) and successfully ran: R CMD javareconf now, I am getting the following error: --- . . . checking Java support in R... present: interpreter : '/usr/java/../bin/java' archiver: '/usr/java/../bin/jar' compiler: '/usr/java/../bin/javac' header prep.: '' cpp flags : '' java libs : '-L/usr/java/jdk1.6.0_19/jre/lib/amd64/server -L/usr/java/jdk1.6.0_19/jre/lib/amd64 -L/usr/java/jdk1.6.0 _19/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm' configure: error: One or more Java configuration variables are not set. Make sure R is configured with full Java support (including JDK). Run R CMD javareconf as root to add Java support to R. If you don't have root privileges, run R CMD javareconf -e to set all Java-related variables and then install rJava. as I said previously R CMD javareconf was ran. As suggested by the error message I also tried to run: R CMD javareconf -e although it ran without error it didn't help? What are these configuration variables and how do we set them? Anyone has and idea on how to fix this? Thanks for your support, Gérald Jean Conseiller senior en statistiques, VP Actuariat et Solutions d'assurances, Desjardins Groupe d'Assurances Générales télephone: (418) 835-4900 poste (7639) télecopieur : (418) 835-6657 courrier électronique: gerald.j...@dgag.ca We believe in God, others must bring Data. W. Edwards Deming Le message ci-dessus, ainsi que les documents l'accompagnant, sont destinés uniquement aux personnes identifiées et peuvent contenir des informations privilégiées, confidentielles ou ne pouvant être divulguées. Si vous avez reçu ce message par erreur, veuillez le détruire. This communication ( and/or the attachments ) is intended for named recipients only and may contain privileged or confidential information which is not to be disclosed. If you received this communication by mistake please destroy all copies. Faites bonne impression et imprimez seulement au besoin ! Think green before you print ! Le message ci-dessus, ainsi que les documents l'accompagnant, sont destinés uniquement aux personnes identifiées et peuvent contenir des informations privilégiées, confidentielles ou ne pouvant être divulguées. Si vous avez reçu ce message par erreur, veuillez le détruire. This communication (and/or the attachments) is intended for named recipients only and may contain privileged or confidential information which is not to be disclosed. If you received this communication by mistake please destroy all copies. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] for loop; lm() regressions; list of vectors - lapply - accolades and square brackets??
On Mar 31, 2010, at 9:13 AM, Driss Agramelal wrote: Hello and thank you both for your answers! Dennis, I tried to simply run lm(a ~ b) after re-importing a as a matrix, but I get the following error message: Error in model.frame.default(formula = a ~ b, drop.unused.levels = TRUE) : invalid type (list) for variable 'a' so maybe I have to specify something in the arguments? What do you think? David, I tried your syntax as well, and received quasi-the same error statement: for(i in seq_along(a)) print(r - lm(a[i] ~ b) ) Error in model.frame.default(formula = a[i] ~ b, drop.unused.levels = TRUE) : invalid type (list) for variable 'a[i]' I am not too familiar with the use of accolades, square brackets and parentheses, the order in which they have to come in the function and the role they play, but I think they might be important... I also tried to use lapply; it works wonderfully for a basic function like: lapply(a, mean) I get a list of results with names and values..perfect! But with the lm() function... I just don't know how to write the arguments... tried several options without success... Any idea that could help me solve this only seemingly easy task would be most welcome!! Do you think we can figure this out when you have provided no sample data and have not provided even the results of str on the data object you are working with? Generally one gains insight by parring the problem down to smaller test cases and working with them. Perhaps the first 5 elements of a rather than all 150? -- David. 2010/3/30 David Winsemius dwinsem...@comcast.net On Mar 30, 2010, at 12:42 PM, Driss Agramelal wrote: ## Hello everyone, ## ## I am trying to execute 150 times a lm regression using the 'for' loop, with 150 vectors for y, ## ## and always the same vector for x. ## ## I have an object with 150 elements named a, ## ## and a vector of 60 values named b. ## ## Each element in a has 60 values plus a header. ## ## When I type: r - lm(i ~ b) for(i in a) print(r) Try instead something like this untested modification: for(i in seq_along(a)) print(r - lm(a[i] ~ b) ) ## I get 150 times the lm results of the first element of a regressed with b, ## ## whereas I would like to have 150 different regression results from each element in a... ## ## Can someone please help me with the syntax of my loop please? ## ## Many Thanks, ## ## Driss Agramelal ## ## Switzerland ## [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT Hi: Did you try lm(a ~ b) ? According to the lm() help page, if a is a matrix, lm will regress each column of the matrix on the right hand side of the formula. Sounds like what you want... HTH, Dennis David Winsemius, MD West Hartford, CT [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error singular gradient matrix at initial parameter estimates in nls
Try the function called `nls.lm' which is contained in the minpack.lm package. See if it solves your problem. Ravi. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Corrado Sent: Wednesday, March 31, 2010 9:13 AM Cc: r-help@r-project.org Subject: Re: [R] Error singular gradient matrix at initial parameter estimates in nls Dear JN, Bert, 1) It is not a perfect fit. I do not think I have ever said that. I said that an external algorithms fits the model without any problems: with ~ 500,000 data points and 19 paramters (ki in the original equation), it fits the model in less than 1 second. The data are not artificial data. The variables are independent (pi in the original model). The solution is unique and the rapidity of convergence is practically independent from the selection of start conditions (with a reasonable selection of start conditions at least). The resulting residuals are approximately normally distributed with mean 0 and sd ~ 4.23. 2) I agree with the comment of Bert on over-parametrization, but again the model is not overparamterised, and it is identifiable (in part answered already in (1)) Regards Prof. John C Nash wrote: If you have a perfect fit, you have zero residuals. But in the nls manual page we have: Warning: *Do not use ‘nls’ on artificial zero-residual data.* So this is a case of complaining that your diesel car is broken because you ignored the Diesel fuel only sign on the filler cap and put in gasoline. However I've not been happy with this choice in the code of nls -- it's been there a long time -- and my own codes from 1974 onwards have always handled zero residual cases. I do believe that the code could at least give a better diagnostic message. Zero residuals -- perfect fits -- arise when one is interested more or less in an interpolating function rather than doing statistics, and I can understand the reluctance of statisticians to countenance such a use of nls. And Bert's comment on overparametrization is almost certainly valid also. JN -- Corrado Topi PhD Researcher Global Climate Change and Biodiversity Area 18,Department of Biology University of York, York, YO10 5YW, UK Phone: + 44 (0) 1904 328645, E-mail: ct...@york.ac.uk __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] (no subject)
The answer depends on what your goals are. If you are simply trying to put all the hazard ratios on a similar scale, then I often use the HR comparing risk of a subject at the 25th percentile to one at the 75th percentile. This has already been suggested by David W. But this is not perfect. The key issue is that a definition of important is slippery. Is a risk factor that increases your death rate 3-fold but only appears in 10% of the subjects more or less important than one that confers a 50% increase of risk but in 1/2 the subjects? (Smoking confers a major increase in the risk of a rare disease -lung cancer- and a more modest increase in the risk of heart disease. The second generates more excess deaths than the first. Which to highlight is an old debate in public health.) Frank's answer went more to the issue of statistical importance, which is a yet another dimension. Terry T. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ggplot2: Adding points to a density plot
Thanks a lot! This got me started! Joh Dennis Murphy wrote: Hi: Try this: library(ggplot2) movmed - ddply(movies, .(decade), summarise, med = median(rating)) m + geom_point(data = movmed, aes(x = med), y = 0, size = 2) HTH, Dennis On Wed, Mar 31, 2010 at 4:46 AM, Johannes Graumann johannes_graum...@web.de wrote: Hi, Consider something like library(ggplot2) movies$decade - round_any(movies$year, 10) m - qplot(rating,data=movies,colour=factor(decade),geom=density) m (modified from ?stat_density). I'd like to add on the line y=0 a dot for the median of each decade category (using the same colour coding as the fill). I'm failing miserably at all my m + geom_point based approaches and would appreciate if someone could show me the ggplot2 way of achieving this. Thanks, Joh __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem comparing hazard ratios
Frank, Is there an article that discusses this idea of bootstrapping the ranks of the likelihood ratio chi-square Statistics to assess relative importance of predictors in time-to-event data (specifically Cox PH model)? Thanks, Ravi. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Frank E Harrell Jr Sent: Tuesday, March 30, 2010 3:57 PM To: Michal Figurski Cc: r-help@r-project.org Subject: Re: [R] Problem comparing hazard ratios Michal Figurski wrote: Dear R-Helpers, I am a novice in survival analysis. I have the following code: for (i in 3:12) print(coxph(Surv(time, status)~a[,i], data=a)) I used it to fit the Cox Proportional Hazard models separately for every available parameter (columns 3:12) in my data set - with intention to compare the Hazard Ratios. However, some of my variables are in range 0.1 to 1.6, others in range 5000 to 9000. How do I compare HRs between such variables? I have rescaled all the variables to be in 0 to 1 range - is this the proper way to go? Is there a way to somehow calculate the same HRs (as for rescaled parameters) from the HRs for original parameters? Many thanks in advance. There are a lot of issues related to this that will require a good bit of study, both in survival analysis and in regression. I would start with bootstrapping the ranks of the likelihood ratio chi-square statistics of the competing biomarkers. Frank -- Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error grid must have equal distances in each direction
M Joshi, I don't know but I guess that some might have looked at your previous thread on 14 March (also about the geoR package). You received help and good advice then, but it doesn't appear that you are following it. It appears to be a similar problem this time. Also, this list is the wrong place for that question. Please read the posting guide to find out the correct place. Its a question about a package. HTH, Matthew maddy madhura1...@gmail.com wrote in message news:1269974076132-1745651.p...@n4.nabble.com... Hello All, Can anyone please help me on this error? Error in FUN(X[[1L]], ...) : different grid distances detected, but the grid must have equal distances in each direction -- try gridtriple=TRUE that avoids numerical errors. The program that I am trying to run posted in the previous post of this thread.After the rows 1021 of my matrix of size 1024*1024, I start getting all the values as 0s. How to set the gridtriple as I am using the grf function which does not take this parameter as input. The maximum vector limit that can be reached in 'R' is 2^30, why does it not allow me to create arrays of length even of size 2^17? Thanks, M Joshi -- View this message in context: http://n4.nabble.com/Error-grid-must-have-equal-distances-in-each-direction-tp1695189p1745651.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] regular expression help to extract specific strings from text
strapply in gsubfn can extract matches based on content which seems to
be what you want:
library(gsubfn)
f - function(...) sapply(list(...), paste, collapse = , )
DF - data.frame(x,
Source = strapply(x, ^(\\w+):, c, simplify = f),
Mentions = strapply(x, @(\\w+), c, simplify = f),
HashTags = strapply(x, #(\\w+), c, simplify = f))
DF[DF == ] - NA
On Wed, Mar 31, 2010 at 9:20 AM, Tony B tony.bre...@googlemail.com wrote:
Dear all,
Lets say I have the following:
x - c(Eve: Going to try something new today..., Adam: Hey @Eve, how are
you finding R? #rstats, Eve: @Adam, It's awesome, so much better at
statistics that #Excel ever was! @Cain @Able disagree though :(, Adam:
@Eve I'm sure they'll sort it out :), blahblah)
x
[1] Eve: Going to try something new
today...
[2] Adam: Hey @Eve, how are you finding R?
#rstats
[3] Eve: @Adam, It's awesome, so much better at statistics that
\n#Excel ever was! @Cain @Able disagree though :(
[4] Adam: @Eve I'm sure they'll sort it
out :)
[5] blahblah
I would like to come up with a data frame which looks like this
(pulling out the usernames and #tags):
data.frame(Msg = x, Source = c(Eve, Adam, Eve, Adam, NA), Mentions =
c(NA, Eve, Adam, Cain, Able, Eve, NA), HashTags = c(NA, rstats,
Excel, NA, NA))
The best I can do so far is:
source - lapply(x, function (x) {
tmp - strsplit(x, :, fixed = TRUE)
if(length(tmp[[1]]) 2) {
tmp - c(NA, tmp)
}
return(tmp[[1]][1])
} )
source - unlist(source)
[1] Eve Adam Eve Adam NA
I can't work out how to extract the usernames starting with '@' or the
#tags. I can identify them using gsub and replace them, but I don't
know how to just extract those terms only, e.g. sort of the opposite
of the following
gsub(@([A-Za-z0-9_]+), @[...], x)
[1] Eve: Going to try something new today...
[2] Adam: Hey @[...], how are you finding R? #rstats
[3] Eve: @[...], It's awesome, so much better at statistics that
#Excel ever was! @[...] @[...] disagree though :(
[4] Adam: @[...] I'm sure they'll sort it out :)
[5] blahblah
and
gsub(#([A-Za-z0-9_]+), #[...], x)
[1] Eve: Going to try something new today...
[2] Adam: Hey @Eve, how are you finding R? #[...]
[3] Eve: @Adam, It's awesome, so much better at statistics that
#[...] ever was! @Cain @Able disagree though :(
[4] Adam: @Eve I'm sure they'll sort it out :)
[5] blahblah
I hope that makes sense, and thank you kindly in advance for your
time.
Tony Breyal
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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and provide commented, minimal, self-contained, reproducible code.
[R] library sets: A EMPTY does not work; gset_intersection(A,EMPTY) works
When using generalized sets from sets library
A EMPTY does not work, but gset_intersection(A,EMPTY) works: example
code below
Is it a bug?
Best regards,
Ryszard
library(sets)
support - universe - c('a','b','c','d')
A - gset(support=support, memberships=c(0.2, 0.2, 0.9, 0),
universe=universe)
class(A)
A
E - A - A # create empty set
I - gset_intersection(A, E) # this WORKS
class(I); I
I - A E # this DOES NOT WORK
# ---
support - universe - c('a','b','c','d')
A - gset(support=support, memberships=c(0.2, 0.2, 0.9, 0),
universe=universe)
class(A)
[1] gset cset
A
{a [0.2], b [0.2], c [0.9]}
E - A - A
I - gset_intersection(A, E) # this WORKS
class(I); I
[1] set gset cset
{}
I - A E # this DOES NOT WORK
Error in A E :
operations are possible only for numeric or logical types
In addition: Warning message:
Incompatible methods (Ops.gset, Ops.set) for
--
Confidentiality Notice: This message is private and may ...{{dropped:8}}
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] regular expression help to extract specific strings from text
On Wed, Mar 31, 2010 at 8:20 AM, Tony B tony.bre...@googlemail.com wrote: Dear all, Lets say I have the following: x - c(Eve: Going to try something new today..., Adam: Hey @Eve, how are you finding R? #rstats, Eve: @Adam, It's awesome, so much better at statistics that #Excel ever was! @Cain @Able disagree though :(, Adam: @Eve I'm sure they'll sort it out :), blahblah) x [1] Eve: Going to try something new today... [2] Adam: Hey @Eve, how are you finding R? #rstats [3] Eve: @Adam, It's awesome, so much better at statistics that \n#Excel ever was! @Cain @Able disagree though :( [4] Adam: @Eve I'm sure they'll sort it out :) [5] blahblah I would like to come up with a data frame which looks like this (pulling out the usernames and #tags): data.frame(Msg = x, Source = c(Eve, Adam, Eve, Adam, NA), Mentions = c(NA, Eve, Adam, Cain, Able, Eve, NA), HashTags = c(NA, rstats, Excel, NA, NA)) You can do this pretty easily with the stringr package: library(stringr) str_extract_all(x, @[a-zA-z]+) sapply(str_extract_all(x, @[a-zA-z]+), str_c, collapse = , ) Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Question about 'logit' and 'mlogit' in Zelig
Abraham, This appears to be your 3rd unanswered post to r-help in March, all 3 have been about the Zelig package. Please read the posting guide and find out the correct place to send questions about packages. Then you might get an answer. HTH Matthew Mathew, Abraham T amat...@ku.edu wrote in message news:281f7a5fdfef844696011cb21185f8ac0be...@mailbox-11.home.ku.edu... I'm running a multinomial logit in R using the Zelig packages. According to str(trade962a), my dependent variable is a factor with three levels. When I run the multinomial logit I get an error message. However, when I run 'model=logit' it works fine. any ideas on whats wrong? ## MULTINOMIAL LOGIT anes96two - zelig(trade962a ~ age962 + education962 + personal962 + economy962 + partisan962 + employment962 + union962 + home962 + market962 + race962 + income962, model=logit, data=data96) summary(anes96two) #Error in attr(tt, depFactors)$depFactorVar : # $ operator is invalid for atomic vectors ## LOGIT Call: zelig(formula = trade962a ~ age962 + education962 + personal962 + economy962 + partisan962 + employment962 + union962 + home962 + market962 + race962 + income962, model = logit, data = data96) Deviance Residuals: Min 1Q Median 3Q Max -2.021 -1.179 0.764 1.032 1.648 Coefficients: Estimate Std. Error z value Pr(|z|) (Intercept) -0.697675 0.600991 -1.161 0.2457 age962 0.003235 0.004126 0.784 0.4330 education962 -0.065198 0.038002 -1.716 0.0862 . personal9620.006827 0.072421 0.094 0.9249 economy962-0.200535 0.084554 -2.372 0.0177 * partisan9620.092361 0.079005 1.169 0.2424 employment962 -0.009346 0.044106 -0.212 0.8322 union962 -0.016293 0.149887 -0.109 0.9134 home962 -0.150221 0.133685 -1.124 0.2611 market962 0.292320 0.128636 2.272 0.0231 * race9620.205828 0.094890 2.169 0.0301 * income962 0.263363 0.048275 5.455 4.89e-08 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 1841.2 on 1348 degrees of freedom Residual deviance: 1746.3 on 1337 degrees of freedom (365 observations deleted due to missingness) AIC: 1770.3 Number of Fisher Scoring iterations: 4 Thanks Abraham __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] tm package- remove stowords failling
Hi, I just noticed that by inspecting the matrix term that no all stopwords are removed, does someone know how to fix that? library(tm) data(crude) d-tm_map(crude, removeWords, stopwords(language='english')) dt-DocumentTermMatrix(d,control=list(minWordLength=3, minDocFreq=2)) inspect( dt) I am using R version 2.10, tm package 0.5-3 cheers Welma [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] You are right and the problem is solved. Re: about the possible errors in Rgraphviz Package
Based on your success I thought I would try again. I am not sure why I had more success this time but this time I got this far even though I did not change my path at all or make any system changes from what I had before. I did reinstall Rgraphviz but used the previously installed graphviz. I tried this code taken from the Rgrpahviz vignette: library(Rgraphviz) Loading required package: graph Loading required package: grid set.seed(123) V - letters[1:10] M - 1:4 g1 - randomGraph(V, M, 0.2) g1 A graphNEL graph with undirected edges Number of Nodes = 10 Number of Edges = 16 but when I tried to plot it R crashed. plot(g1) It did produce this message on the Windows console (not the R console): Error: Layout type: dot not recognized. Use one of: There was nothing after the of: R.version.string [1] R version 2.10.1 Patched (2010-03-10 r51276) win.version() [1] Windows Vista (build 6002) Service Pack 2 packageDescription(Rgraphviz)$Version [1] 1.24.0 graphvizVersion() $installed_version [1] ‘2.20.3’ $build_version [1] ‘2.20.3’ On Wed, Mar 31, 2010 at 9:56 AM, HU,ZHENGJUN h...@ufl.edu wrote: Hi Martin, It is really a 'PATH' problem. After adding C:\Program Files\Graphviz2.20\bin to the 'PATH' environment variable, the Rgraphviz package can be loaded without any error messages. Sorry that I ONLY set my 'PATH' environment variable correctly for R but not for Graphviz. Thank you and Duncan so much for your great help. Howard On Tue Mar 30 18:12:54 EDT 2010, Martin Morgan mtmor...@fhcrc.org wrote: On 03/30/2010 03:06 PM, HU,ZHENGJUN wrote: Hi Martin, I am 100% sure that I set my 'PATH' environment variable correctly because all other packages can loaded correctly as well as because R can be run correctly under both MS DOS and MS Windows XP. Also, I can create some simple R packages correctly. The PATH must be set correctly to include graphviz, as in my example below. Copy and paste the output of strsplit(Sys.getenv(PATH), ;) and list.files(strsplit(Sys.getenv(PATH), ;)[[1]][[14]], dll) Martin Thanks. Howard On Tue Mar 30 16:58:55 EDT 2010, Martin Morgan mtmor...@fhcrc.org wrote: On 03/30/2010 01:13 PM, HU,ZHENGJUN wrote: Hi Martin, I uninstalled graphviz-2.26.3.msi and then installed graphviz-2.20.3.1.msi. Then installed the Rgraphviz package again. As expected, I got the same error messages as before: Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/R-210~1.1/library/Rgraphviz/libs/Rgraphviz.dll': LoadLibrary failure: The specified module could not be found. 'LoadLibrary' is being vague, the 'specified modules' are the DLLs from graphviz. Have you checked that your 'PATH' environment variable is set correctly? In R strsplit(Sys.getenv(PATH), ;) $PATH ... [14] C:\\Program Files\\Graphviz2.20\\bin ... The relevant files in this directory might look like list.files(strsplit(Sys.getenv(PATH), ;)[[1]][[14]], dll) [1] iconv.dll intl.dll [3] jpeg62.dll libcairo-2.dll [5] libcdt-4.dll libcgraph-4.dll [7] libexpat.dll libfontconfig-1.dll [9] libfreetype-6.dll libgdk_pixbuf-2.0-0.dll [11] libglib-2.0-0.dll libgmodule-2.0-0.dll [13] libgobject-2.0-0.dll libgraph-4.dll [15] libgvc-4.dll libgvplugin_core-5.dll [17] libgvplugin_dot_layout-5.dll libgvplugin_gd-5.dll [19] libgvplugin_neato_layout-5.dll libgvplugin_pango-5.dll [21] libltdl-3.dll libpango-1.0-0.dll [23] libpangocairo-1.0-0.dll libpangoft2-1.0-0.dll [25] libpangowin32-1.0-0.dll libpathplan-4.dll [27] libpng12.dll libxml2.dll Martin Thank you. Howard On Tue Mar 30 15:36:05 EDT 2010, Martin Morgan mtmor...@fhcrc.org wrote: On 03/30/2010 10:24 AM, HU,ZHENGJUN wrote: Hi Duncan, (They are pretty hard to find, but I think you can find them on the Bioconductor site.) It is not enough to install the Rgraphviz package, you also need to install Graphviz. Yes I did. Before installing the Rgraphviz package successfully, (1) I downloaded graphviz-2.26.3.msi for MS Windows (XP) and installed it successfully and (2) I also installed the packages from Bioconductor by: (Note: I use MS Windows XP and R 2.10.1 version) This is a bioconductor package so please ask on the Bioconductor mailing list http://bioconductor.org/docs/mailList.html See the 'README' file in the 'tar.gz' file at http://bioconductor.org/packages/release/Software.html http://bioconductor.org/packages/2.5/bioc/html/Rgraphviz.html http://bioconductor.org/packages/2.5/bioc/src/contrib/Rgraphviz_1.24.0.tar.gz which says o. install Graphviz ***2.20.3.1*** Windows ***binary*** distribution from http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.1.msi you must use this version
Re: [R] zero standard errors with geeglm in geepack
You may not have got an answer because you posted to the wrong place. Its a question about a package. Please read the posting guide. miriza miri...@sfwmd.gov wrote in message news:1269886286228-1695430.p...@n4.nabble.com... Hi! I am using geeglm to fit a Poisson model to a timeseries of count data as follows. Since there are no clusters I use 73 values of 1 for the ids. The problem I have is that I am getting standard errors of zero for the parameters. What am I doing wrong? Thanks, Michelle N_Base [1] 95 85 104 88 102 104 91 88 85 115 96 83 91 107 96 116 118 103 89 88 101 117 82 80 83 103 115 119 95 90 82 91 108 115 93 96 72 [38] 98 95 98 97 104 86 107 92 94 95 100 107 76 104 101 80 102 100 91 96 89 71 109 97 113 99 127 115 91 81 73 69 92 90 78 57 Year [1] 1932 1933 1934 1935 1936 1937 1938 1939 1940 1941 1942 1943 1944 1945 1946 1947 1948 1949 1950 1951 1952 1953 1954 1955 1956 1957 1958 1959 1960 1961 [31] 1962 1963 1964 1965 1966 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 [61] 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2006 tes=geese(formula = N_Base ~ Year, id = rep(1, 73), family = poisson, corstr = ar1) summary(tes) Call: geese(formula = N_Base ~ Year, id = rep(1, 73), family = poisson, corstr = ar1) Mean Model: Mean Link: log Variance to Mean Relation: poisson Coefficients: estimate san.se wald p (Intercept) 7.1131 0 Inf 0 Year -0.0013 0 Inf 0 Scale Model: Scale Link:identity Estimated Scale Parameters: estimate san.se wald p (Intercept) 1.79 0 Inf 0 Correlation Model: Correlation Structure: ar1 Correlation Link: identity Estimated Correlation Parameters: estimate san.se wald p alpha0.187 0 Inf 0 Returned Error Value:0 Number of clusters: 1 Maximum cluster size: 73 -- View this message in context: http://n4.nabble.com/zero-standard-errors-with-geeglm-in-geepack-tp1695430p1695430.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] GEE for a timeseries of count (one cluster)
Contact the authors of those packages ? miriza miri...@sfwmd.gov wrote in message news:1269981675252-1745896.p...@n4.nabble.com... Hi! I was wondering if there were any packages that would allow me to fit a GEE to a single timeseries of counts so that I could account for autocorrelation in the data. I tried gee, geepack and yags packages, but I do not get standard errors for the parameters when using a single cluster. Any tips? Thanks, Michelle -- View this message in context: http://n4.nabble.com/GEE-for-a-timeseries-of-count-one-cluster-tp1745896p1745896.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] for loop; lm() regressions; list of vectors - lapply - accolades and square brackets??
Driss, David is right - you should include data/code. Nevertheless, the error you get suggests that what you call a matrix is in fact a data.frame; that's usually a crucial distinction. There are two things you might try: Dennis' way: lm(as.matrix(a) ~ b) David's way: for(i in seq_along(a)) print(r- lm(a[ ,i] ~ b) ) #Note the comma! -Peter Ehlers On 2010-03-31 7:42, David Winsemius wrote: On Mar 31, 2010, at 9:13 AM, Driss Agramelal wrote: Hello and thank you both for your answers! Dennis, I tried to simply run lm(a ~ b) after re-importing a as a matrix, but I get the following error message: Error in model.frame.default(formula = a ~ b, drop.unused.levels = TRUE) : invalid type (list) for variable 'a' so maybe I have to specify something in the arguments? What do you think? David, I tried your syntax as well, and received quasi-the same error statement: for(i in seq_along(a)) print(r- lm(a[i] ~ b) ) Error in model.frame.default(formula = a[i] ~ b, drop.unused.levels = TRUE) : invalid type (list) for variable 'a[i]' I am not too familiar with the use of accolades, square brackets and parentheses, the order in which they have to come in the function and the role they play, but I think they might be important... I also tried to use lapply; it works wonderfully for a basic function like: lapply(a, mean) I get a list of results with names and values..perfect! But with the lm() function... I just don't know how to write the arguments... tried several options without success... Any idea that could help me solve this only seemingly easy task would be most welcome!! Do you think we can figure this out when you have provided no sample data and have not provided even the results of str on the data object you are working with? Generally one gains insight by parring the problem down to smaller test cases and working with them. Perhaps the first 5 elements of a rather than all 150? -- Peter Ehlers University of Calgary __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] mcmcglmm starting value example
Apparently not, since this your 3rd unanswered thread to r-help this month about this package. Please read the posting guide and find out where you should send questions about packages. Then you might get an answer. ping chen chen1984...@yahoo.com.cn wrote in message news:975148.47160...@web15304.mail.cnb.yahoo.com... Hi R-users: Can anyone give an example of giving starting values for MCMCglmm? I can't find any anywhere. I have 1 random effect (physicians, and there are 50 of them) and family=ordinal. How can I specify starting values for my fixed effects? It doesn't seem to have the option to do so. Thanks, Ping __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] You are right and the problem is solved. Re: about the possible errors in Rgraphviz Package
By the way, just in case you did not read the entire message R crashed when I tried to run the code from the vignette. On Wed, Mar 31, 2010 at 10:52 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: Based on your success I thought I would try again. I am not sure why I had more success this time but this time I got this far even though I did not change my path at all or make any system changes from what I had before. I did reinstall Rgraphviz but used the previously installed graphviz. I tried this code taken from the Rgrpahviz vignette: library(Rgraphviz) Loading required package: graph Loading required package: grid set.seed(123) V - letters[1:10] M - 1:4 g1 - randomGraph(V, M, 0.2) g1 A graphNEL graph with undirected edges Number of Nodes = 10 Number of Edges = 16 but when I tried to plot it R crashed. plot(g1) It did produce this message on the Windows console (not the R console): Error: Layout type: dot not recognized. Use one of: There was nothing after the of: R.version.string [1] R version 2.10.1 Patched (2010-03-10 r51276) win.version() [1] Windows Vista (build 6002) Service Pack 2 packageDescription(Rgraphviz)$Version [1] 1.24.0 graphvizVersion() $installed_version [1] ‘2.20.3’ $build_version [1] ‘2.20.3’ On Wed, Mar 31, 2010 at 9:56 AM, HU,ZHENGJUN h...@ufl.edu wrote: Hi Martin, It is really a 'PATH' problem. After adding C:\Program Files\Graphviz2.20\bin to the 'PATH' environment variable, the Rgraphviz package can be loaded without any error messages. Sorry that I ONLY set my 'PATH' environment variable correctly for R but not for Graphviz. Thank you and Duncan so much for your great help. Howard On Tue Mar 30 18:12:54 EDT 2010, Martin Morgan mtmor...@fhcrc.org wrote: On 03/30/2010 03:06 PM, HU,ZHENGJUN wrote: Hi Martin, I am 100% sure that I set my 'PATH' environment variable correctly because all other packages can loaded correctly as well as because R can be run correctly under both MS DOS and MS Windows XP. Also, I can create some simple R packages correctly. The PATH must be set correctly to include graphviz, as in my example below. Copy and paste the output of strsplit(Sys.getenv(PATH), ;) and list.files(strsplit(Sys.getenv(PATH), ;)[[1]][[14]], dll) Martin Thanks. Howard On Tue Mar 30 16:58:55 EDT 2010, Martin Morgan mtmor...@fhcrc.org wrote: On 03/30/2010 01:13 PM, HU,ZHENGJUN wrote: Hi Martin, I uninstalled graphviz-2.26.3.msi and then installed graphviz-2.20.3.1.msi. Then installed the Rgraphviz package again. As expected, I got the same error messages as before: Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/R-210~1.1/library/Rgraphviz/libs/Rgraphviz.dll': LoadLibrary failure: The specified module could not be found. 'LoadLibrary' is being vague, the 'specified modules' are the DLLs from graphviz. Have you checked that your 'PATH' environment variable is set correctly? In R strsplit(Sys.getenv(PATH), ;) $PATH ... [14] C:\\Program Files\\Graphviz2.20\\bin ... The relevant files in this directory might look like list.files(strsplit(Sys.getenv(PATH), ;)[[1]][[14]], dll) [1] iconv.dll intl.dll [3] jpeg62.dll libcairo-2.dll [5] libcdt-4.dll libcgraph-4.dll [7] libexpat.dll libfontconfig-1.dll [9] libfreetype-6.dll libgdk_pixbuf-2.0-0.dll [11] libglib-2.0-0.dll libgmodule-2.0-0.dll [13] libgobject-2.0-0.dll libgraph-4.dll [15] libgvc-4.dll libgvplugin_core-5.dll [17] libgvplugin_dot_layout-5.dll libgvplugin_gd-5.dll [19] libgvplugin_neato_layout-5.dll libgvplugin_pango-5.dll [21] libltdl-3.dll libpango-1.0-0.dll [23] libpangocairo-1.0-0.dll libpangoft2-1.0-0.dll [25] libpangowin32-1.0-0.dll libpathplan-4.dll [27] libpng12.dll libxml2.dll Martin Thank you. Howard On Tue Mar 30 15:36:05 EDT 2010, Martin Morgan mtmor...@fhcrc.org wrote: On 03/30/2010 10:24 AM, HU,ZHENGJUN wrote: Hi Duncan, (They are pretty hard to find, but I think you can find them on the Bioconductor site.) It is not enough to install the Rgraphviz package, you also need to install Graphviz. Yes I did. Before installing the Rgraphviz package successfully, (1) I downloaded graphviz-2.26.3.msi for MS Windows (XP) and installed it successfully and (2) I also installed the packages from Bioconductor by: (Note: I use MS Windows XP and R 2.10.1 version) This is a bioconductor package so please ask on the Bioconductor mailing list http://bioconductor.org/docs/mailList.html See the 'README' file in the 'tar.gz' file at http://bioconductor.org/packages/release/Software.html http://bioconductor.org/packages/2.5/bioc/html/Rgraphviz.html
Re: [R] library sets: A EMPTY does not work; gset_intersection(A,EMPTY) works
Unless I'm missing something, I don't see any method
in pkg:sets for intersection other than gset_intersection.
So you're using the base R function `` whose help page
tells you that its arguments should be vectors. Yours
aren't.
-Peter Ehlers
On 2010-03-31 8:50, Czerminski, Ryszard wrote:
When using generalized sets from sets library
A EMPTY does not work, but gset_intersection(A,EMPTY) works: example
code below
Is it a bug?
Best regards,
Ryszard
library(sets)
support- universe- c('a','b','c','d')
A- gset(support=support, memberships=c(0.2, 0.2, 0.9, 0),
universe=universe)
class(A)
A
E- A - A # create empty set
I- gset_intersection(A, E) # this WORKS
class(I); I
I- A E # this DOES NOT WORK
# ---
support- universe- c('a','b','c','d')
A- gset(support=support, memberships=c(0.2, 0.2, 0.9, 0),
universe=universe)
class(A)
[1] gset cset
A
{a [0.2], b [0.2], c [0.9]}
E- A - A
I- gset_intersection(A, E) # this WORKS
class(I); I
[1] set gset cset
{}
I- A E # this DOES NOT WORK
Error in A E :
operations are possible only for numeric or logical types
In addition: Warning message:
Incompatible methods (Ops.gset, Ops.set) for
--
Confidentiality Notice: This message is private and may ...{{dropped:8}}
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Peter Ehlers
University of Calgary
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Simplifying particular piece of code
On Wed, Mar 31, 2010 at 5:11 PM, Sergey Goriatchev serg...@gmail.com wrote:
but
data - merge(data,data.list)
works.
Neither data or data.list is a list, so do.call does not work.
I am very weak on lists, never used them before
Best,
Sergey
Hej Sergey,
Ok; I was wondering if the apply thing would work. Cool that merge
would be clever enough to append a matrix. I'm guessing that you've
got what you needed then? For reference, (and for the general list) I
had changed the code before Sergeys response, replacing apply() with
lapply(). That code follows below.
Best regards,
Gustaf
-
cnames - c(BMM, GM1, IYC, FCA, IMM, BME, CRT, GTF,
ERU, ERE, EPT, EVA, EMT, EMM, EMV, ETM)
AVnames - paste(cnames, .AV120, sep=)
SDnames - paste(cnames, .SD120, sep=)
a - zoo(matrix(rep(seq(from=160, to=10, by=-10), 1000), ncol=16, byrow=TRUE))
colnames(a) - AVnames
b - zoo(matrix(rep(2, 16000), ncol=16))
colnames(b) - SDnames
data - merge(a, b)
MyFunc - function(x, ret, stdev){
if(any(is.na(c(x[ret], x[stdev]{
return(NA)
}else{
return(x[ret]/x[stdev])
}
}
names.df-data.frame(rbind(SRnames,AVnames,SDnames))
func - function(.names){
apply(data, 1, MyFunc, ret=.names[2], stdev=.names[3])
}
data.list-lapply(names.df, func)
mrets-do.call(merge,c(list(data),data.list))
On Wed, Mar 31, 2010 at 12:33, Gustaf Rydevik gustaf.ryde...@gmail.com wrote:
How about this (not tested, since you did not provide example data nor
function code):
---
SRnames - paste(colnames.mrets, .SR, sep=)
AVnames - paste(colnames.mrets, .AV120, sep=)
SDnames - paste(colnames.mrets, .SD120, sep=)
names.matrix-cbind(SRnames,AVnames,SDnames)
mrets.list-apply(names.matrix,1,function(.names){
apply(mrets,1,MyFunc,ret=.names[2],stdev=.names[3]}
)
names(mrets.list)-names.matrix[,1]
mrets-do.call(merge,mrets.list)
-
?
/Gustaf
On Wed, Mar 31, 2010 at 12:10 PM, Sergey Goriatchev serg...@gmail.com wrote:
Hello, everyone
I have a piece of code that looks like this:
mrets - merge(mrets, BMM.SR=apply(mrets, 1, MyFunc, ret=BMM.AV120,
stdev=BMM.SD120))
mrets - merge(mrets, GM1.SR=apply(mrets, 1, MyFunc, ret=GM1.AV120,
stdev=GM1.SD120))
mrets - merge(mrets, IYC.SR=apply(mrets, 1, MyFunc, ret=IYC.AV120,
stdev=IYC.SD120))
mrets - merge(mrets, FCA.SR=apply(mrets, 1, MyFunc, ret=FCA.AV120,
stdev=FCA.SD120))
mrets - merge(mrets, IMM.SR=apply(mrets, 1, MyFunc, ret=IMM.AV120,
stdev=IMM.SD120))
mrets - merge(mrets, BME.SR=apply(mrets, 1, MyFunc, ret=BME.AV120,
stdev=BME.SD120))
mrets - merge(mrets, CRT.SR=apply(mrets, 1, MyFunc, ret=CRT.AV120,
stdev=CRT.SD120))
mrets - merge(mrets, GTF.SR=apply(mrets, 1, MyFunc, ret=GTF.AV120,
stdev=GTF.SD120))
mrets - merge(mrets, ERU.SR=apply(mrets, 1, MyFunc, ret=ERU.AV120,
stdev=ERU.SD120))
mrets - merge(mrets, ERE.SR=apply(mrets, 1, MyFunc, ret=ERE.AV120,
stdev=ERE.SD120))
mrets - merge(mrets, EPT.SR=apply(mrets, 1, MyFunc, ret=EPT.AV120,
stdev=EPT.SD120))
mrets - merge(mrets, EVA.SR=apply(mrets, 1, MyFunc, ret=EVA.AV120,
stdev=EVA.SD120))
mrets - merge(mrets, EMT.SR=apply(mrets, 1, MyFunc, ret=EMT.AV120,
stdev=EMT.SD120))
mrets - merge(mrets, EMM.SR=apply(mrets, 1, MyFunc, ret=EMM.AV120,
stdev=EMM.SD120))
mrets - merge(mrets, EMV.SR=apply(mrets, 1, MyFunc, ret=EMV.AV120,
stdev=EMV.SD120))
mrets - merge(mrets, ETM.SR=apply(mrets, 1, MyFunc, ret=ETM.AV120,
stdev=ETM.SD120))
Is there a way to simplify this, some sort of loop?
mrets is a zoo object.
.AV120 and .SD120 are columns in this object.
I need the exact .SR column names.
This does not work:
SRnames - paste(colnames.mrets, .SR, sep=)
AVnames - paste(colnames.mrets, .AV120, sep=)
SDnames - paste(colnames.mrets, .SD120, sep=)
for(i in seq(SRnames)){
mrets - merge(mrets, SRnames[i]=apply(mrets, 1, MyFunc,
ret=AVnames[i], stdev=SDnames[i]))
}
Help much appreciated.
Regards,
Sergey
--
Simplicity is the last step of art./Bruce Lee
The more you know, the more you know you don't know. /Myself
I'm not young enough to know everything. /Oscar Wilde
Experience is one thing you can't get for nothing. /Oscar Wilde
When you are finished changing, you're finished. /Benjamin Franklin
Luck is where preparation meets opportunity. /George Patten
Kniven skärpes bara mot stenen.
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tel: +46(0)703 051 451
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skype:gustaf_rydevik
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[R] predict.Arima: warnings from xreg magic
When I run predict.Arima in my code, I get warnings like:
Warning message:
In cbind(intercept = rep(1, n), xreg) :
number of rows of result is not a multiple of vector length (arg 1)
I think this is because I'm not running predict.Arima in the same
environment that I did the fit, so the data object used in the fit is no
longer present. Looking at the predict.Arima source,
predict.Arima -
function (object, n.ahead = 1, newxreg = NULL, se.fit = TRUE, ...)
{
myNCOL - function(x) if (is.null(x)) 0 else NCOL(x)
rsd - object$residuals
xr - object$call$xreg
xreg - if (!is.null(xr)) eval.parent(xr) else NULL
ncxreg - myNCOL(xreg)
if (myNCOL(newxreg) != ncxreg)
stop('xreg' and 'newxreg' have different numbers of columns)
class(xreg) - NULL
xtsp - tsp(rsd)
n - length(rsd)
arma - object$arma
coefs - object$coef
narma - sum(arma[1L:4L])
if (length(coefs) narma) {
if (names(coefs)[narma + 1L] == intercept) {
xreg - cbind(intercept = rep(1, n), xreg)
newxreg - cbind(intercept = rep(1, n.ahead), newxreg)
ncxreg - ncxreg + 1L
}
...
It looks to me as if it assumes that object$call$xreg is available in
the current (well, parent) environment.
To add insult to injury, it doesn't look like xreg is used anywhere in
the code; it's calculated, then ignored.
So, here are my questions:
1. Is this a correct diagnosis?
2. What can I do about it?
a. Is there a version of arima with less magic?
b. Should I try to populate my environment to look like the calling
environment?
c. Other?
Thanks,
Johann
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Re: [R] Simplifying particular piece of code
Thanks for help, Gustaf!
(Kan man säga man tackar oxa?) :-)
On Wed, Mar 31, 2010 at 17:34, Gustaf Rydevik gustaf.ryde...@gmail.com wrote:
On Wed, Mar 31, 2010 at 5:11 PM, Sergey Goriatchev serg...@gmail.com wrote:
but
data - merge(data,data.list)
works.
Neither data or data.list is a list, so do.call does not work.
I am very weak on lists, never used them before
Best,
Sergey
Hej Sergey,
Ok; I was wondering if the apply thing would work. Cool that merge
would be clever enough to append a matrix. I'm guessing that you've
got what you needed then? For reference, (and for the general list) I
had changed the code before Sergeys response, replacing apply() with
lapply(). That code follows below.
Best regards,
Gustaf
-
cnames - c(BMM, GM1, IYC, FCA, IMM, BME, CRT, GTF,
ERU, ERE, EPT, EVA, EMT, EMM, EMV, ETM)
AVnames - paste(cnames, .AV120, sep=)
SDnames - paste(cnames, .SD120, sep=)
a - zoo(matrix(rep(seq(from=160, to=10, by=-10), 1000), ncol=16, byrow=TRUE))
colnames(a) - AVnames
b - zoo(matrix(rep(2, 16000), ncol=16))
colnames(b) - SDnames
data - merge(a, b)
MyFunc - function(x, ret, stdev){
if(any(is.na(c(x[ret], x[stdev]{
return(NA)
}else{
return(x[ret]/x[stdev])
}
}
names.df-data.frame(rbind(SRnames,AVnames,SDnames))
func - function(.names){
apply(data, 1, MyFunc, ret=.names[2], stdev=.names[3])
}
data.list-lapply(names.df, func)
mrets-do.call(merge,c(list(data),data.list))
On Wed, Mar 31, 2010 at 12:33, Gustaf Rydevik gustaf.ryde...@gmail.com
wrote:
How about this (not tested, since you did not provide example data nor
function code):
---
SRnames - paste(colnames.mrets, .SR, sep=)
AVnames - paste(colnames.mrets, .AV120, sep=)
SDnames - paste(colnames.mrets, .SD120, sep=)
names.matrix-cbind(SRnames,AVnames,SDnames)
mrets.list-apply(names.matrix,1,function(.names){
apply(mrets,1,MyFunc,ret=.names[2],stdev=.names[3]}
)
names(mrets.list)-names.matrix[,1]
mrets-do.call(merge,mrets.list)
-
?
/Gustaf
On Wed, Mar 31, 2010 at 12:10 PM, Sergey Goriatchev serg...@gmail.com
wrote:
Hello, everyone
I have a piece of code that looks like this:
mrets - merge(mrets, BMM.SR=apply(mrets, 1, MyFunc, ret=BMM.AV120,
stdev=BMM.SD120))
mrets - merge(mrets, GM1.SR=apply(mrets, 1, MyFunc, ret=GM1.AV120,
stdev=GM1.SD120))
mrets - merge(mrets, IYC.SR=apply(mrets, 1, MyFunc, ret=IYC.AV120,
stdev=IYC.SD120))
mrets - merge(mrets, FCA.SR=apply(mrets, 1, MyFunc, ret=FCA.AV120,
stdev=FCA.SD120))
mrets - merge(mrets, IMM.SR=apply(mrets, 1, MyFunc, ret=IMM.AV120,
stdev=IMM.SD120))
mrets - merge(mrets, BME.SR=apply(mrets, 1, MyFunc, ret=BME.AV120,
stdev=BME.SD120))
mrets - merge(mrets, CRT.SR=apply(mrets, 1, MyFunc, ret=CRT.AV120,
stdev=CRT.SD120))
mrets - merge(mrets, GTF.SR=apply(mrets, 1, MyFunc, ret=GTF.AV120,
stdev=GTF.SD120))
mrets - merge(mrets, ERU.SR=apply(mrets, 1, MyFunc, ret=ERU.AV120,
stdev=ERU.SD120))
mrets - merge(mrets, ERE.SR=apply(mrets, 1, MyFunc, ret=ERE.AV120,
stdev=ERE.SD120))
mrets - merge(mrets, EPT.SR=apply(mrets, 1, MyFunc, ret=EPT.AV120,
stdev=EPT.SD120))
mrets - merge(mrets, EVA.SR=apply(mrets, 1, MyFunc, ret=EVA.AV120,
stdev=EVA.SD120))
mrets - merge(mrets, EMT.SR=apply(mrets, 1, MyFunc, ret=EMT.AV120,
stdev=EMT.SD120))
mrets - merge(mrets, EMM.SR=apply(mrets, 1, MyFunc, ret=EMM.AV120,
stdev=EMM.SD120))
mrets - merge(mrets, EMV.SR=apply(mrets, 1, MyFunc, ret=EMV.AV120,
stdev=EMV.SD120))
mrets - merge(mrets, ETM.SR=apply(mrets, 1, MyFunc, ret=ETM.AV120,
stdev=ETM.SD120))
Is there a way to simplify this, some sort of loop?
mrets is a zoo object.
.AV120 and .SD120 are columns in this object.
I need the exact .SR column names.
This does not work:
SRnames - paste(colnames.mrets, .SR, sep=)
AVnames - paste(colnames.mrets, .AV120, sep=)
SDnames - paste(colnames.mrets, .SD120, sep=)
for(i in seq(SRnames)){
mrets - merge(mrets, SRnames[i]=apply(mrets, 1, MyFunc,
ret=AVnames[i], stdev=SDnames[i]))
}
Help much appreciated.
Regards,
Sergey
--
Simplicity is the last step of art./Bruce Lee
The more you know, the more you know you don't know. /Myself
I'm not young enough to know everything. /Oscar Wilde
Experience is one thing you can't get for nothing. /Oscar Wilde
When you are finished changing, you're finished. /Benjamin Franklin
Luck is where preparation meets opportunity. /George Patten
Kniven skärpes bara mot stenen.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Gustaf Rydevik, M.Sci.
tel: +46(0)703 051 451
address:Essingetorget 40,112 66 Stockholm, SE
Re: [R] library sets: A EMPTY does not work; gset_intersection(A,EMPTY) works
On 2010-03-31 9:30, Peter Ehlers wrote:
Unless I'm missing something, I don't see any method
in pkg:sets for intersection other than gset_intersection.
Whoops, a bit quick on the draw.
There are of course also set_intersection and cset_intersection,
but not AFAICS any method for ``.
-Peter Ehlers
So you're using the base R function `` whose help page
tells you that its arguments should be vectors. Yours
aren't.
-Peter Ehlers
On 2010-03-31 8:50, Czerminski, Ryszard wrote:
When using generalized sets from sets library
A EMPTY does not work, but gset_intersection(A,EMPTY) works: example
code below
Is it a bug?
Best regards,
Ryszard
library(sets)
support- universe- c('a','b','c','d')
A- gset(support=support, memberships=c(0.2, 0.2, 0.9, 0),
universe=universe)
class(A)
A
E- A - A # create empty set
I- gset_intersection(A, E) # this WORKS
class(I); I
I- A E # this DOES NOT WORK
# ---
support- universe- c('a','b','c','d')
A- gset(support=support, memberships=c(0.2, 0.2, 0.9, 0),
universe=universe)
class(A)
[1] gset cset
A
{a [0.2], b [0.2], c [0.9]}
E- A - A
I- gset_intersection(A, E) # this WORKS
class(I); I
[1] set gset cset
{}
I- A E # this DOES NOT WORK
Error in A E :
operations are possible only for numeric or logical types
In addition: Warning message:
Incompatible methods (Ops.gset, Ops.set) for
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[R] Boundary kernel for kernel density plot?
Hello, Is a kernel called the boundary kernel available for kernel density plots? In the help, I can only see the following kernels: gaussian, rectangular, triangular, epanechnikov, biweight, cosine or optcosine. The boundary kernel apparently improves the estimate in a neighborhood of zero. Thanks, Ravi Kulkarni -- View this message in context: http://n4.nabble.com/Boundary-kernel-for-kernel-density-plot-tp1746968p1746968.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] position of mismatches in all.equal()?
I've actually found a solution to my problem. In case someone could be interested, the which() function seems to do the trick: test2$let2 - factor(test2$let2, levels=letters[1:10]) which(test1[,3]!=test2[,3]) [1] 7 which(test1[,1:3]!=test2[,1:3]) [1] 27 Le 3/31/2010 15:13, Ivan Calandra a écrit : Dear R users, I would like to compare two dataframes, actually their categorical variables (as factors) only (there are 12, from column 1 to 12). The reason I do that is that I got 2 datasets from two different methods and I would like to be sure that each method used the same data (3D images) to extract 2 different sets of 3D parameters. Is it clear so far? So I thought about using all.equal() like this: test1 - data.frame(num=1:10, let1=letters[1:10], let2=letters[1:10]) test2 - data.frame(num=1:10, let1=letters[1:10], let2=letters[c(1:6, 6, 8:10)]) Since I want to compare only some columns, I do this: all.equal(test1[,1:2], test2[,1:2]) [1] TRUE all.equal(test1[,1:3], test2[,1:3]) [1] Component 3: Attributes: Component 2: Lengths (10, 9) differ (string compare on first 9) [2] Component 3: Attributes: Component 2: 3 string mismatches [3] Component 3: 1 string mismatch If I get TRUE, then everythin's fine. But if not, I just know from the output in which column(s) are the mismatches and how many (here 1). But my datasets are 2000+ rows, and I would like to know the row number(s) where mismatches occur. How can I do that? Thank you for your help! Regards, Ivan -- Ivan CALANDRA PhD Student University of Hamburg Biozentrum Grindel und Zoologisches Museum Abt. Säugetiere Martin-Luther-King-Platz 3 D-20146 Hamburg, GERMANY +49(0)40 42838 6231 ivan.calan...@uni-hamburg.de ** http://www.for771.uni-bonn.de http://webapp5.rrz.uni-hamburg.de/mammals/eng/mitarbeiter.php __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] library sets: A EMPTY does not work; gset_intersection(A,EMPTY) works
It seems that A B works the same way as gset_intersection(A,B)
as long as A and B are not empty...
see below:
fuzzy_logic(Yager, p=2)
support - universe - c('a','b','c','d')
A - gset(support=support, memberships=c(0.2, 0.2, 0.9, 0),
universe=universe)
B - gset(support=support, memberships=c(0.211, 0.222, 0.999, 0),
universe=universe)
A
B
A B
gset_intersection(A,B)
E - A - A
A E
gset_intersection(A,E)
fuzzy_logic(Yager, p=2)
support - universe - c('a','b','c','d')
A - gset(support=support, memberships=c(0.2, 0.2, 0.9, 0),
universe=universe)
B - gset(support=support, memberships=c(0.211, 0.222, 0.999, 0),
universe=universe)
A
{a [0.2], b [0.2], c [0.9]}
B
{a [0.211], b [0.222], c [0.999]}
A B
{c [0.85]}
gset_intersection(A,B)
{c [0.85]}
E - A - A
A E
Error in A E :
operations are possible only for numeric or logical types
In addition: Warning message:
Incompatible methods (Ops.gset, Ops.set) for
gset_intersection(A,E)
{}
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-Original Message-
From: Peter Ehlers [mailto:ehl...@ucalgary.ca]
Sent: Wednesday, March 31, 2010 11:43 AM
To: Czerminski, Ryszard
Cc: R-help@r-project.org
Subject: Re: [R] library sets: A EMPTY does not work;
gset_intersection(A,EMPTY) works
On 2010-03-31 9:30, Peter Ehlers wrote:
Unless I'm missing something, I don't see any method
in pkg:sets for intersection other than gset_intersection.
Whoops, a bit quick on the draw.
There are of course also set_intersection and cset_intersection,
but not AFAICS any method for ``.
-Peter Ehlers
So you're using the base R function `` whose help page
tells you that its arguments should be vectors. Yours
aren't.
-Peter Ehlers
On 2010-03-31 8:50, Czerminski, Ryszard wrote:
When using generalized sets from sets library
A EMPTY does not work, but gset_intersection(A,EMPTY) works: example
code below
Is it a bug?
Best regards,
Ryszard
library(sets)
support- universe- c('a','b','c','d')
A- gset(support=support, memberships=c(0.2, 0.2, 0.9, 0),
universe=universe)
class(A)
A
E- A - A # create empty set
I- gset_intersection(A, E) # this WORKS
class(I); I
I- A E # this DOES NOT WORK
# ---
support- universe- c('a','b','c','d')
A- gset(support=support, memberships=c(0.2, 0.2, 0.9, 0),
universe=universe)
class(A)
[1] gset cset
A
{a [0.2], b [0.2], c [0.9]}
E- A - A
I- gset_intersection(A, E) # this WORKS
class(I); I
[1] set gset cset
{}
I- A E # this DOES NOT WORK
Error in A E :
operations are possible only for numeric or logical types
In addition: Warning message:
Incompatible methods (Ops.gset, Ops.set) for
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...{{dropped:8}}
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University of Calgary
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Re: [R] Error singular gradient matrix at initial parameter estimates in nls
Corrado: Over parameterization/non-identifiability is not determined by the ratio of the number of data values to the number of parameters: if you try to fit a scatter of a zillion points that lie near a straight line to a model with curvature -- the 4p logistic function, say -- you're over-parameterized. Period. I am not an expert on nonlinear optimization, but I would think that the correlation matrix of the parameters would be one thing to check; another would be the change in the fits when some of the model terms are dropped. But model selection for nonlinear fitting is not a trivial issue, and those with real expertise, not me, could be more helpful. The fact that other algorithms converge while R's did not is also not particularly informative, I believe. This could occur merely due to the choice of convergence criteria (step size, choice of objective function, etc.). Or the convergence could be to a local minimum, not a global one. Comparison of performance of optimization algorithms is, again, a cottage industry for which serious expertise is required. (This should not be taken as a defense of R, either. My optimization ignorance cuts both ways). So I do not think your protestations of innocence are necessarily accurate. Nor, I agree, are my accusations of guilt. I **still** believe that your convergence difficulties are due to over-parameterization, and that this is something that needs to be carefully investigated; but that is a prior, not a posterior. Examining lots of plots is probably a good place to begin. Cheers, Bert Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Corrado Sent: Wednesday, March 31, 2010 6:13 AM Cc: r-help@r-project.org Subject: Re: [R] Error singular gradient matrix at initial parameter estimates in nls Dear JN, Bert, 1) It is not a perfect fit. I do not think I have ever said that. I said that an external algorithms fits the model without any problems: with ~ 500,000 data points and 19 paramters (ki in the original equation), it fits the model in less than 1 second. The data are not artificial data. The variables are independent (pi in the original model). The solution is unique and the rapidity of convergence is practically independent from the selection of start conditions (with a reasonable selection of start conditions at least). The resulting residuals are approximately normally distributed with mean 0 and sd ~ 4.23. 2) I agree with the comment of Bert on over-parametrization, but again the model is not overparamterised, and it is identifiable (in part answered already in (1)) Regards Prof. John C Nash wrote: If you have a perfect fit, you have zero residuals. But in the nls manual page we have: Warning: *Do not use 'nls' on artificial zero-residual data.* So this is a case of complaining that your diesel car is broken because you ignored the Diesel fuel only sign on the filler cap and put in gasoline. However I've not been happy with this choice in the code of nls -- it's been there a long time -- and my own codes from 1974 onwards have always handled zero residual cases. I do believe that the code could at least give a better diagnostic message. Zero residuals -- perfect fits -- arise when one is interested more or less in an interpolating function rather than doing statistics, and I can understand the reluctance of statisticians to countenance such a use of nls. And Bert's comment on overparametrization is almost certainly valid also. JN -- Corrado Topi PhD Researcher Global Climate Change and Biodiversity Area 18,Department of Biology University of York, York, YO10 5YW, UK Phone: + 44 (0) 1904 328645, E-mail: ct...@york.ac.uk __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] You are right and the problem is solved. Re: about the possible errors in Rgraphviz Package
On 03/31/2010 08:18 AM, Gabor Grothendieck wrote: By the way, just in case you did not read the entire message R crashed I think you mean that you got an error message, not that R became unusable? More below... when I tried to run the code from the vignette. On Wed, Mar 31, 2010 at 10:52 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: Based on your success I thought I would try again. I am not sure why I had more success this time but this time I got this far even though I did not change my path at all or make any system changes from what I had before. I did reinstall Rgraphviz but used the previously installed graphviz. I tried this code taken from the Rgrpahviz vignette: library(Rgraphviz) Loading required package: graph Loading required package: grid set.seed(123) V - letters[1:10] M - 1:4 g1 - randomGraph(V, M, 0.2) g1 A graphNEL graph with undirected edges Number of Nodes = 10 Number of Edges = 16 but when I tried to plot it R crashed. plot(g1) It did produce this message on the Windows console (not the R console): Error: Layout type: dot not recognized. Use one of: In the past this has come about when accessing incorrect graphviz DLLs. The gory detail (if I remember correctly) is that a FILE* gets allocated in Rgraphviz and passed to graphviz, and if there is a compiler mismatch then there are no guarantees about FILE* representation. The implication is that your Rgraphviz and graphiz are at least partly out of sync, but it could also be that I am 'getting lucky'. When you say (quoting from above)... did not change my path at all or make any system changes from what I the implication is that your PATH was already set to include a graphviz2.20\\bin directory; I'd encourage you to confirm that. And recognizing that you might justifiably be willing to put this on the shelf, you might also use Dependency Walker (http://www.dependencywalker.com/) to open the Rgraphviz DLL (R_HOME/libraries/Rgraphviz/libs/Rgraphviz.dll), right click on the RGRAPHVIZ.DLL showing up in the top left panel, and choose 'Full paths', and verify that LIBCDT-4.DLL, LIBGRAPH-4.DLL, and LIBGVC-4.DLL all point to Graphviz2.20\bin. Martin There was nothing after the of: R.version.string [1] R version 2.10.1 Patched (2010-03-10 r51276) win.version() [1] Windows Vista (build 6002) Service Pack 2 packageDescription(Rgraphviz)$Version [1] 1.24.0 graphvizVersion() $installed_version [1] ‘2.20.3’ $build_version [1] ‘2.20.3’ On Wed, Mar 31, 2010 at 9:56 AM, HU,ZHENGJUN h...@ufl.edu wrote: Hi Martin, It is really a 'PATH' problem. After adding C:\Program Files\Graphviz2.20\bin to the 'PATH' environment variable, the Rgraphviz package can be loaded without any error messages. Sorry that I ONLY set my 'PATH' environment variable correctly for R but not for Graphviz. Thank you and Duncan so much for your great help. Howard On Tue Mar 30 18:12:54 EDT 2010, Martin Morgan mtmor...@fhcrc.org wrote: On 03/30/2010 03:06 PM, HU,ZHENGJUN wrote: Hi Martin, I am 100% sure that I set my 'PATH' environment variable correctly because all other packages can loaded correctly as well as because R can be run correctly under both MS DOS and MS Windows XP. Also, I can create some simple R packages correctly. The PATH must be set correctly to include graphviz, as in my example below. Copy and paste the output of strsplit(Sys.getenv(PATH), ;) and list.files(strsplit(Sys.getenv(PATH), ;)[[1]][[14]], dll) Martin Thanks. Howard On Tue Mar 30 16:58:55 EDT 2010, Martin Morgan mtmor...@fhcrc.org wrote: On 03/30/2010 01:13 PM, HU,ZHENGJUN wrote: Hi Martin, I uninstalled graphviz-2.26.3.msi and then installed graphviz-2.20.3.1.msi. Then installed the Rgraphviz package again. As expected, I got the same error messages as before: Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/R-210~1.1/library/Rgraphviz/libs/Rgraphviz.dll': LoadLibrary failure: The specified module could not be found. 'LoadLibrary' is being vague, the 'specified modules' are the DLLs from graphviz. Have you checked that your 'PATH' environment variable is set correctly? In R strsplit(Sys.getenv(PATH), ;) $PATH ... [14] C:\\Program Files\\Graphviz2.20\\bin ... The relevant files in this directory might look like list.files(strsplit(Sys.getenv(PATH), ;)[[1]][[14]], dll) [1] iconv.dll intl.dll [3] jpeg62.dll libcairo-2.dll [5] libcdt-4.dll libcgraph-4.dll [7] libexpat.dll libfontconfig-1.dll [9] libfreetype-6.dll libgdk_pixbuf-2.0-0.dll [11] libglib-2.0-0.dll libgmodule-2.0-0.dll [13] libgobject-2.0-0.dll libgraph-4.dll [15] libgvc-4.dll libgvplugin_core-5.dll [17] libgvplugin_dot_layout-5.dll libgvplugin_gd-5.dll [19] libgvplugin_neato_layout-5.dll
Re: [R] GLM / large dataset question
Geelman, This appears to be your first post to this list. Welcome to R. Nearly 2 days is quite a long time to wait though, so you are unlikely to get a reply now. Feedback : the question seems quite vague and imprecise. It depends on which R you mean (32bit/64bit) and how much ram you have. It also depends on your data and what you want to do with it. Did you mean 100.000 (i.e. one hundred) or 100,000. Also, '8000 explanatory variables' seems a lot, especially to be stored in 'a factor'. There is no R code in your post so we can't tell if you're using glm correctly or not. You could provide the result of object.size(), and dim() on your data rather than explaining it in words. No reply often, but not always, means you haven't followed some detail of the posting guide or haven't followed this : http://www.catb.org/~esr/faqs/smart-questions.html. HTH Matthew geelman geel...@zonnet.nl wrote in message news:mkedkcmimcmgohidffmbieklcaaa.geel...@zonnet.nl... LS, How large a dataset can glm fit with a binomial link function? I have a set of about 100.000 observations and about 8000 explanatory variables (a factor with 8000 levels). Is there a way to find out how large datasets R can handle in general? Thanks in advance, geelman __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] dot plot
Hi kayj kayj schrieb: Also, I do nto know how to combine two plots into one plot? Have a look at ?par . There is some argument add or new (i am not sure) that you have to set to TRUE after making the first plot and then you can add a second plot with running plot() once more. thanks and I appreciate your help You are welcome. You should search the archive of the help list a bit more extensively before posting as this question has been asked several times already (this happened to me as well already ;-)). Best Jannis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Off Topic: teenie weenie numbers -- Was: Precision level
I spoke with a theoretical physicist and he said he encountered 10^-120. Has something to do with attempts to describe/explain the universe... Dimitri On Fri, Mar 26, 2010 at 2:33 PM, Steve Lianoglou mailinglist.honey...@gmail.com wrote: On Fri, Mar 26, 2010 at 1:11 PM, Barry Rowlingson b.rowling...@lancaster.ac.uk wrote: On Fri, Mar 26, 2010 at 4:31 PM, Bert Gunter gunter.ber...@gene.com wrote: *** COMPLETELY OFF TOPIC *** Although machine precision (smallest numerical values that can be exactly represented) is important for numerical calculations, what is the smallest number that anyone has actually seen describing physical phenomena in science? I've seen values of ca. 1e-20 or so routinely used in physics on both size (e.g quarks) and time scales (lifetimes of evanescent particles). Beyond that about the smallest values I've seen are about 1e-40 or so seconds in discussions of Big Bang dynamics. Does anyone know of smaller ones (and those I've quoted might certainly be off somewhat). Hmmm smaller than 1e40... Well, I think I've seen the charge on an electron given as much, much smaller than that... Here's another: after ~4 years of graduate school, Citibank is starting to send me bank statements using these numbers to quantify the amount of $$ I have in the bank ... Oh, I just earned $.02 interest? ... thanks for the email notification, Citibank! Just curious. Hope this abuse of the list is not too egregious. Ignore if you think it is. It's Casual Friday. :-) -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dimitri Liakhovitski Ninah.com dimitri.liakhovit...@ninah.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Comparing times in two time zones
I have data that is collected in two different time zones z$OnDateTime - as.POSIXct(runway$OnDateTime, tz = EST5EDT, format=%m/%d/%Y %H:%M) is in Eastern time, and zi$ActualOnLocal - as.POSIXct(oooi$ActualOnLocal, tz=MST7MDT, format=%m/%d/%Y %H:%M) is in Mountain. I converted the runway time to Mountain (I think) z$OnDateTime = format(runway$OnDateTime, tz=MST7MDT) The corresponding times in the two data sets seem identical (within a few minutes) when printed out: ] z$ActualOnLocal[1:5] [1] 2008-11-01 07:49:00 MDT 2008-11-03 07:58:00 MST [3] 2008-11-04 08:04:00 MST 2008-11-05 07:44:00 MST [5] 2008-11-06 07:32:00 MST z$OnDateTime[1:5] [1] 2008-11-01 07:49:00 2008-11-03 07:57:00 2008-11-04 08:04:00 [4] 2008-11-05 07:43:00 2008-11-06 07:32:00 But when I do z$dt= as.numeric(difftime(z$ActualOnLocal, z$OnDateTime, units=mins)) the difference is 120 minutes. How do I get my date times so that difftime works properly? Thanks, Jim Rome __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] library sets: A EMPTY does not work; gset_intersection(A,EMPTY) works
Ryszard,
You've made me take a closer look and now I do think that
you've found a bug.
After a quick look at the package vignette, I see that the
authors have indeed overloaded and so it should work for
your example. The problem seems to be the order of the class
attribute which is used to call the relevant 'Ops' function:
class(A)
#[1] gset cset
class(B)
#[1] gset cset
class(E - A - A)
#[1] set gset cset
If you re-order the class vector, function Ops.gset will be called
to handle A and E:
class(E) - class(E)[c(2,3,1)]
A E
#{}
I've cc'd David Meyer.
-Peter Ehlers
On 2010-03-31 10:11, Czerminski, Ryszard wrote:
It seems that A B works the same way as gset_intersection(A,B)
as long as A and B are not empty...
see below:
fuzzy_logic(Yager, p=2)
support- universe- c('a','b','c','d')
A- gset(support=support, memberships=c(0.2, 0.2, 0.9, 0),
universe=universe)
B- gset(support=support, memberships=c(0.211, 0.222, 0.999, 0),
universe=universe)
A
B
A B
gset_intersection(A,B)
E- A - A
A E
gset_intersection(A,E)
fuzzy_logic(Yager, p=2)
support- universe- c('a','b','c','d')
A- gset(support=support, memberships=c(0.2, 0.2, 0.9, 0),
universe=universe)
B- gset(support=support, memberships=c(0.211, 0.222, 0.999, 0),
universe=universe)
A
{a [0.2], b [0.2], c [0.9]}
B
{a [0.211], b [0.222], c [0.999]}
A B
{c [0.85]}
gset_intersection(A,B)
{c [0.85]}
E- A - A
A E
Error in A E :
operations are possible only for numeric or logical types
In addition: Warning message:
Incompatible methods (Ops.gset, Ops.set) for
gset_intersection(A,E)
{}
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-Original Message-
From: Peter Ehlers [mailto:ehl...@ucalgary.ca]
Sent: Wednesday, March 31, 2010 11:43 AM
To: Czerminski, Ryszard
Cc: R-help@r-project.org
Subject: Re: [R] library sets: A EMPTY does not work;
gset_intersection(A,EMPTY) works
On 2010-03-31 9:30, Peter Ehlers wrote:
Unless I'm missing something, I don't see any method
in pkg:sets for intersection other than gset_intersection.
Whoops, a bit quick on the draw.
There are of course also set_intersection and cset_intersection,
but not AFAICS any method for ``.
-Peter Ehlers
So you're using the base R function `` whose help page
tells you that its arguments should be vectors. Yours
aren't.
-Peter Ehlers
On 2010-03-31 8:50, Czerminski, Ryszard wrote:
When using generalized sets from sets library
A EMPTY does not work, but gset_intersection(A,EMPTY) works: example
code below
Is it a bug?
Best regards,
Ryszard
library(sets)
support- universe- c('a','b','c','d')
A- gset(support=support, memberships=c(0.2, 0.2, 0.9, 0),
universe=universe)
class(A)
A
E- A - A # create empty set
I- gset_intersection(A, E) # this WORKS
class(I); I
I- A E # this DOES NOT WORK
# ---
support- universe- c('a','b','c','d')
A- gset(support=support, memberships=c(0.2, 0.2, 0.9, 0),
universe=universe)
class(A)
[1] gset cset
A
{a [0.2], b [0.2], c [0.9]}
E- A - A
I- gset_intersection(A, E) # this WORKS
class(I); I
[1] set gset cset
{}
I- A E # this DOES NOT WORK
Error in A E :
operations are possible only for numeric or logical types
In addition: Warning message:
Incompatible methods (Ops.gset, Ops.set) for
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[R] Bar plots with bars made of stacked text
I would like to make bar plots where the bars are composed of text like this: http://www.thomaslevine.com/lowres/text_bars.png Is there a package that will help me with this? Thanks Tom __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] interpretation of p values for highly correlated logistic analysis
Hi Claus, welcome to the wonderful world of collinearity (or multicollinearity, as some call it)! You have a near linear relationship between some of your predictors, which can (and in your case does) lead to extreme parameter estimates, which in some cases almost cancel out (a coefficient of +/-40 on a categorical variable in logistic regression is a lot, and the intercept and two of the roman parameter estimates almost cancel out) but which are rather unstable (hence your high p-values). Belsley, Kuh and Welsch did some work on condition indices and variance decomposition proportions, and variance inflation factors are quite popular for diagnosing multicollinearity - google these terms for a bit, and enlightenment will surely follow. What can you do? You should definitely think long and hard about your data. Should you be doing separate regressions for some factor levels? Should you drop a factor from the analysis? Should you do a categorical analogue of Principal Components Analysis on your data before the regression? I personally have never done this, but correspondence analysis has been recommended as a discrete alternative to PCA on this list, see a couple of books by M. J. Greenacre. Best of luck! Stephan claus orourke schrieb: Dear list, I want to perform a logistic regression analysis with multiple categorical predictors (i.e., a logit) on some data where there is a very definite relationship between one predicator and the response/independent variable. The problem I have is that in such a case the p value goes very high (while I as a naive newbie would expect it to crash towards 0). I'll illustrate my problem with some toy data. Say I have the following data as an input frame: roman animal colour 1 alphadog black 2 betacat white 3 alphadog black 4 alphacat black 5 betadog white 6 alphacat black 7 gammadog white 8 alphacat black 9 gammadog white 10 betacat white 11 alphadog black 12 alphacat black 13 gammadog white 14 alphacat black 15 betadog white 16 betacat black 17 alphacat black 18 betadog white In this toy data you can see that roman:alpha and roman:beta are pretty good predictors of colour Let's say I perform logistic analysis directly on the raw data with colour as a response variable: options(contrasts=c(contr.treatment,contr.poly)) anal1 - glm(data$colour~data$roman+data$animal,family=binomial) then I find that my P values for each individual level coefficient approach 1: Coefficients: Estimate Std. Error z value Pr(|z|) (Intercept) -41.65 19609.49 -0.0020.998 data$romanbeta 42.35 19609.49 0.0020.998 data$romangamma43.74 31089.48 0.0010.999 data$animaldog 20.48 13866.00 0.0010.999 while I expect the p value for roman:beta to be quite low because it is a good predictor of colour:white On the other hand, if I then run an anova with a Chi-sq test on the result model, I find as I would expect that 'roman' is a good predictor of colour. anova(anal1,test=Chisq) Analysis of Deviance Table Model: binomial, link: logit Response: data$colour Terms added sequentially (first to last) Df Deviance Resid. Df Resid. Dev P(|Chi|) NULL 1724.7306 data$roman 2 19.323915 5.4067 6.366e-05 *** data$animal 1 1.587614 3.81910.2077 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Can anyone please explain why my p value is so high for the individual levels? Sorry for what is likely a stupid question. Claus p.s., when I run logistic analysis on data that is more 'randomised' everything comes out as I expect. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] reshaping data
Hi All, Can someone help me reshape following data: Var1 Var2 Val A X 1 A Y 2 A Z 3 B X 4 B Y 5 B Z 6 to some kind of matrix/tabular format (preferably as a matrix), may be like Var1 X Y Z A 1 2 3 B 4 5 6 Any help would be greatly appreciated, Kim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] reshaping data
Try this: xtabs(Val ~ Var1 + Var2, data = x) On Wed, Mar 31, 2010 at 3:23 PM, Kim Jung Hwa kimhwamaill...@gmail.com wrote: Hi All, Can someone help me reshape following data: Var1 Var2 Val A X 1 A Y 2 A Z 3 B X 4 B Y 5 B Z 6 to some kind of matrix/tabular format (preferably as a matrix), may be like Var1 X Y Z A 1 2 3 B 4 5 6 Any help would be greatly appreciated, Kim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] reshaping data
Hi Kim, look at the reshape() command with direction=wide. Or at the reshape package. HTH, Stephan Kim Jung Hwa schrieb: Hi All, Can someone help me reshape following data: Var1 Var2 Val A X 1 A Y 2 A Z 3 B X 4 B Y 5 B Z 6 to some kind of matrix/tabular format (preferably as a matrix), may be like Var1 X Y Z A 1 2 3 B 4 5 6 Any help would be greatly appreciated, Kim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] for loop; lm() regressions; list of vectors - lapply - accolades and square brackets??
Peter, it works!!! Thanks a lot to all of you! Yes I mistook a data.frame for a matrix Now both David's and Dennis' solutions work! I am really a beginner with R, and I think it's a wonderful tool, but sometimes a little difficult to use only learning from the manuals and help files... I hope I didn't pollute the help list! I am really sorry I didn't provide more info from the beginning, and for you to fully understand my question, please find my code hereafter, with a 'copy-pastable' sample of my data: What I did: ## Step 1: Import the data (simplified for example) a - read.table(clipboard, header = TRUE) a a1 a2 a3 a4 a5 1 0.01181 0.01181 0.01181 0.01181 0.01181 2 0.11266 0.10878 0.11217 0.11255 0.11258 3 0.00655 0.00655 0.00655 0.00655 0.00655 4 -0.02956 -0.03098 -0.03006 -0.03243 -0.03244 5 -0.01788 -0.01788 -0.01788 -0.01788 -0.01788 6 -0.01106 0.00083 -0.01172 -0.00328 -0.00328 7 0.00668 0.00668 0.00668 0.00668 0.00668 8 0.06130 0.05779 0.06310 0.06144 0.06146 9 0.01300 0.01300 0.01300 0.01300 0.01300 10 -0.05749 -0.05764 -0.05771 -0.05970 -0.05972 11 -0.04019 -0.04019 -0.04019 -0.04019 -0.04019 12 -0.01223 -0.01235 -0.01229 -0.00866 -0.00867 13 0.01422 0.01422 0.01422 0.01422 0.01422 14 0.00636 0.00603 0.00633 0.00813 0.00813 15 -0.00715 -0.00715 -0.00715 -0.00715 -0.00715 16 -0.02773 -0.03089 -0.02802 -0.02729 -0.02730 17 -0.02534 -0.02534 -0.02534 -0.02534 -0.02534 18 0.01151 0.00634 0.01120 0.01509 0.01509 19 -0.01103 -0.01314 -0.01112 -0.00894 -0.00895 20 -0.01889 -0.01964 -0.01860 -0.01813 -0.01813 21 0.01498 0.01438 0.01526 0.01548 0.01549 22 0.00731 0.00853 0.00746 0.00699 0.00699 23 -0.02229 -0.02069 -0.02247 -0.02223 -0.02224 24 0.00824 0.00817 0.00786 0.00783 0.00783 25 0.00596 0.00699 0.00613 0.00621 0.00622 26 -0.04201 -0.04241 -0.04212 -0.04271 -0.04272 27 0.03012 0.02972 0.03041 0.03056 0.03056 28 -0.00972 -0.01009 -0.00957 -0.01037 -0.01037 29 -0.02637 -0.02657 -0.02598 -0.02614 -0.02615 30 -0.05003 -0.05134 -0.05025 -0.05054 -0.05055 31 -0.02514 -0.02483 -0.02523 -0.02424 -0.02424 32 0.02797 0.02732 0.02802 0.02663 0.02685 33 -0.00777 -0.00791 -0.00766 -0.00716 -0.00716 34 -0.01836 -0.01830 -0.01855 -0.01820 -0.01842 b - c(read.table(clipboard, header = TRUE)) b $b [1] 0.01181 0.02764 0.00655 0.02275 -0.01788 -0.03519 0.00668 0.00541 0.01300 0.01528 -0.04019 [12] -0.00838 0.01422 -0.02362 -0.00715 -0.00862 -0.02534 -0.02361 -0.01210 0.00135 0.00101 -0.00017 [23] -0.02670 0.00799 0.01333 -0.03874 0.04817 -0.00102 -0.02142 -0.04965 -0.02773 0.02451 -0.00953 [34] -0.01985 b - b$b ## Step 2: perform the regressions (David's way) David - *for(i in seq_along(a)) print(r- lm(a[ ,i] ~ b) )* Call: lm(formula = a[, i] ~ b) Coefficients: (Intercept)b 0.00084590.8484054 Call: lm(formula = a[, i] ~ b) Coefficients: (Intercept)b 0.00045230.8215883 Call: lm(formula = a[, i] ~ b) Coefficients: (Intercept)b 0.00085730.8513867 Call: lm(formula = a[, i] ~ b) Coefficients: (Intercept)b 0.001105 0.818247 Call: lm(formula = a[, i] ~ b) Coefficients: (Intercept)b 0.001108 0.818983 ## Step 2: Perform the regressions (Dennis' way) Dennis - *lm(as.matrix(a) ~ b)* Dennis Call: lm(formula = as.matrix(a) ~ b) Coefficients: a1 a2 a3 a4 a5 (Intercept) 0.0008459 0.0004523 0.0008573 0.0011052 0.0011081 b 0.8484054 0.8215883 0.8513867 0.8182470 0.8189826 ## Further steps to come... I am still learning to manipulate my new results to plot.lm a choosen response, to test for autocorrelation, maybe lag or use the gls or robust method, etc... I already did most of the analyses in a test phase with a single regression, but it will be another story on the entire sample...! Maybe I will post some more questions if appropriate...(?) For better comprehension, imagine a1 to a5 are companies, and b is a benchmark index, and I calculate CAPM betas... Many thanks, and I pasted Dennis's answer hereafter for it to be on the forum as well, since it is a valuable contribution!! Driss Agramelal --- Student writing his master's thesis University of St-Gallen Hi: I don't know if this will take care of your problem, but here are several approaches. I'm using the melt() function in package plyr to vectorize the response matrix and create a factor variable from the variable names. Approach 1: lmList() in nlme. library(plyr) library(nlme) df - data.frame(x = 1:10, y1 = rnorm(10), y2 = rnorm(10), y3 = rnorm(10)) # melt() creates a grouping 'variable' to distinguish the responses; the responses # themselves are put into a variable 'value' df1 - melt(df, id.vars = 'x') # Run lmList using variable as the grouping factor... mods - lmList(value ~ x | variable,
Re: [R] reshaping data
Thanks Henrique and Stephan for your reply! Henrique, I'm planning to do some arthitmetic operations on tranformed (matrix) data and then would like to convert it back to original format (as a data frame)... is there an equivalent easy command for this too? Thanks, On Wed, Mar 31, 2010 at 2:26 PM, Henrique Dallazuanna www...@gmail.comwrote: Try this: xtabs(Val ~ Var1 + Var2, data = x) On Wed, Mar 31, 2010 at 3:23 PM, Kim Jung Hwa kimhwamaill...@gmail.com wrote: Hi All, Can someone help me reshape following data: Var1 Var2 Val A X 1 A Y 2 A Z 3 B X 4 B Y 5 B Z 6 to some kind of matrix/tabular format (preferably as a matrix), may be like Var1 X Y Z A 1 2 3 B 4 5 6 Any help would be greatly appreciated, Kim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] reshaping data
Actually, apart from melt() in reshape package. On Wed, Mar 31, 2010 at 2:37 PM, Kim Jung Hwa kimhwamaill...@gmail.comwrote: Thanks Henrique and Stephan for your reply! Henrique, I'm planning to do some arthitmetic operations on tranformed (matrix) data and then would like to convert it back to original format (as a data frame)... is there an equivalent easy command for this too? Thanks, On Wed, Mar 31, 2010 at 2:26 PM, Henrique Dallazuanna www...@gmail.comwrote: Try this: xtabs(Val ~ Var1 + Var2, data = x) On Wed, Mar 31, 2010 at 3:23 PM, Kim Jung Hwa kimhwamaill...@gmail.com wrote: Hi All, Can someone help me reshape following data: Var1 Var2 Val A X 1 A Y 2 A Z 3 B X 4 B Y 5 B Z 6 to some kind of matrix/tabular format (preferably as a matrix), may be like Var1 X Y Z A 1 2 3 B 4 5 6 Any help would be greatly appreciated, Kim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] You are right and the problem is solved. Re: about the possible errors in Rgraphviz Package
I got an error message *AND* R becomes unusable and had to be restarted. Using dependency walker it seems to be complaining about R.dll so I copied all of my ...\R\bin\R*.dll files to .. ...\win-library\2.10\Rgraphviz\libs. Then it complained about IESHIMS.dll so I copied \Program Files\Internet Explorer\IESHIMS.dll to ...\win-library\2.10\Rgraphviz\libs. Looking at dependency walker these DLLs: LIBCDT-4.DLL, LIBGRAPH-4.DLL, and LIBGVC-4.DLL all seem to point to correct place. I still have this message in dependency walker: Warning: At least one module has an unresolved import due to a missing export function in a delay-load dependent module. There is a red mark beside: c:\windows\system32\IEFRAME.DLL but its not missing. I also tried reinstalling R using the latest R 2.10.1. I am still getting the same result, namely I can run the indicated code up to but not including plot(g1) but if I run plot(g1) R crashes and must be restarted. On Wed, Mar 31, 2010 at 12:54 PM, Martin Morgan mtmor...@fhcrc.org wrote: On 03/31/2010 08:18 AM, Gabor Grothendieck wrote: By the way, just in case you did not read the entire message R crashed I think you mean that you got an error message, not that R became unusable? More below... when I tried to run the code from the vignette. On Wed, Mar 31, 2010 at 10:52 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: Based on your success I thought I would try again. I am not sure why I had more success this time but this time I got this far even though I did not change my path at all or make any system changes from what I had before. I did reinstall Rgraphviz but used the previously installed graphviz. I tried this code taken from the Rgrpahviz vignette: library(Rgraphviz) Loading required package: graph Loading required package: grid set.seed(123) V - letters[1:10] M - 1:4 g1 - randomGraph(V, M, 0.2) g1 A graphNEL graph with undirected edges Number of Nodes = 10 Number of Edges = 16 but when I tried to plot it R crashed. plot(g1) It did produce this message on the Windows console (not the R console): Error: Layout type: dot not recognized. Use one of: In the past this has come about when accessing incorrect graphviz DLLs. The gory detail (if I remember correctly) is that a FILE* gets allocated in Rgraphviz and passed to graphviz, and if there is a compiler mismatch then there are no guarantees about FILE* representation. The implication is that your Rgraphviz and graphiz are at least partly out of sync, but it could also be that I am 'getting lucky'. When you say (quoting from above)... did not change my path at all or make any system changes from what I the implication is that your PATH was already set to include a graphviz2.20\\bin directory; I'd encourage you to confirm that. Yes, My path is: PATH=C:\Graphviz2.20\bin;...more stuff... And recognizing that you might justifiably be willing to put this on the shelf, you might also use Dependency Walker (http://www.dependencywalker.com/) to open the Rgraphviz DLL (R_HOME/libraries/Rgraphviz/libs/Rgraphviz.dll), right click on the RGRAPHVIZ.DLL showing up in the top left panel, and choose 'Full paths', and verify that LIBCDT-4.DLL, LIBGRAPH-4.DLL, and LIBGVC-4.DLL all point to Graphviz2.20\bin. Martin There was nothing after the of: R.version.string [1] R version 2.10.1 Patched (2010-03-10 r51276) win.version() [1] Windows Vista (build 6002) Service Pack 2 packageDescription(Rgraphviz)$Version [1] 1.24.0 graphvizVersion() $installed_version [1] ‘2.20.3’ $build_version [1] ‘2.20.3’ On Wed, Mar 31, 2010 at 9:56 AM, HU,ZHENGJUN h...@ufl.edu wrote: Hi Martin, It is really a 'PATH' problem. After adding C:\Program Files\Graphviz2.20\bin to the 'PATH' environment variable, the Rgraphviz package can be loaded without any error messages. Sorry that I ONLY set my 'PATH' environment variable correctly for R but not for Graphviz. Thank you and Duncan so much for your great help. Howard On Tue Mar 30 18:12:54 EDT 2010, Martin Morgan mtmor...@fhcrc.org wrote: On 03/30/2010 03:06 PM, HU,ZHENGJUN wrote: Hi Martin, I am 100% sure that I set my 'PATH' environment variable correctly because all other packages can loaded correctly as well as because R can be run correctly under both MS DOS and MS Windows XP. Also, I can create some simple R packages correctly. The PATH must be set correctly to include graphviz, as in my example below. Copy and paste the output of strsplit(Sys.getenv(PATH), ;) and list.files(strsplit(Sys.getenv(PATH), ;)[[1]][[14]], dll) Martin Thanks. Howard On Tue Mar 30 16:58:55 EDT 2010, Martin Morgan mtmor...@fhcrc.org wrote: On 03/30/2010 01:13 PM, HU,ZHENGJUN wrote: Hi Martin, I uninstalled graphviz-2.26.3.msi and then installed graphviz-2.20.3.1.msi. Then installed the Rgraphviz package again. As expected, I got the same error messages as before: Error in inDL(x,
Re: [R] Off Topic: teenie weenie numbers -- Was: Precision level
There is a story (apocryphal?) about Fred Hoyle, many years ago, having come to the close of a public lecture about his work in Cosmology (I seem to recall that it was to the British Astronomical Association, a society of amateur astronomers, and therefore knowledgeable). He was taking questions. A member of the audience asked (words to the effect): Can Professor Hoyle explain the reasons why he adopted the value 10^1000 [or similar] for the [X] constant? At which Hoyle grinned, and replied ten to the thousand, ten to the two thousand, ten to the three thousand, what difference does it make? Ted. On 31-Mar-10 17:45:54, Dimitri Liakhovitski wrote: I spoke with a theoretical physicist and he said he encountered 10^-120. Has something to do with attempts to describe/explain the universe... Dimitri On Fri, Mar 26, 2010 at 2:33 PM, Steve Lianoglou mailinglist.honey...@gmail.com wrote: On Fri, Mar 26, 2010 at 1:11 PM, Barry Rowlingson b.rowling...@lancaster.ac.uk wrote: On Fri, Mar 26, 2010 at 4:31 PM, Bert Gunter gunter.ber...@gene.com wrote: *** COMPLETELY OFF TOPIC *** Although machine precision (smallest numerical values that can be exactly represented) is important for numerical calculations, what is the smallest number that anyone has actually seen describing physical phenomena in science? I've seen values of ca. 1e-20 or so routinely used in physics on both size (e.g quarks) and time scales (lifetimes of evanescent particles). Beyond that about the smallest values I've seen are about 1e-40 or so seconds in discussions of Big Bang dynamics. Does anyone know of smaller ones (and those I've quoted might certainly be off somewhat). _Hmmm smaller than 1e40... Well, I think I've seen the charge on an electron given as much, much smaller than that... Here's another: after ~4 years of graduate school, Citibank is starting to send me bank statements using these numbers to quantify the amount of $$ I have in the bank ... Oh, I just earned $.02 interest? ... thanks for the email notification, Citibank! Just curious. Hope this abuse of the list is not too egregious. Ignore if you think it is. _It's Casual Friday. :-) -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology _| Memorial Sloan-Kettering Cancer Center _| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dimitri Liakhovitski Ninah.com dimitri.liakhovit...@ninah.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 31-Mar-10 Time: 19:52:35 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] reshaping data
Try: as.data.frame(with(x, tapply(Val, list(Var1, Var2), sum))) On Wed, Mar 31, 2010 at 3:37 PM, Kim Jung Hwa kimhwamaill...@gmail.com wrote: Thanks Henrique and Stephan for your reply! Henrique, I'm planning to do some arthitmetic operations on tranformed (matrix) data and then would like to convert it back to original format (as a data frame)... is there an equivalent easy command for this too? Thanks, On Wed, Mar 31, 2010 at 2:26 PM, Henrique Dallazuanna www...@gmail.com wrote: Try this: xtabs(Val ~ Var1 + Var2, data = x) On Wed, Mar 31, 2010 at 3:23 PM, Kim Jung Hwa kimhwamaill...@gmail.com wrote: Hi All, Can someone help me reshape following data: Var1 Var2 Val A X 1 A Y 2 A Z 3 B X 4 B Y 5 B Z 6 to some kind of matrix/tabular format (preferably as a matrix), may be like Var1 X Y Z A 1 2 3 B 4 5 6 Any help would be greatly appreciated, Kim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] reshaping data
On Mar 31, 2010, at 2:37 PM, Kim Jung Hwa wrote: Thanks Henrique and Stephan for your reply! Henrique, I'm planning to do some arthitmetic operations on tranformed (matrix) data and then would like to convert it back to original format (as a data frame)... is there an equivalent easy command for this too? Thanks, Read the xtabs help page more thoroughly. -- David. On Wed, Mar 31, 2010 at 2:26 PM, Henrique Dallazuanna www...@gmail.com wrote: Try this: xtabs(Val ~ Var1 + Var2, data = x) On Wed, Mar 31, 2010 at 3:23 PM, Kim Jung Hwa kimhwamaill...@gmail.com wrote: Hi All, Can someone help me reshape following data: Var1 Var2 Val A X 1 A Y 2 A Z 3 B X 4 B Y 5 B Z 6 to some kind of matrix/tabular format (preferably as a matrix), may be like Var1 X Y Z A 1 2 3 B 4 5 6 Any help would be greatly appreciated, Kim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] AHRQ Patient Quality Indicators
Is anyone aware of R code that mimic's AHRQ's SAS code for their Prevention Quality Indicators (PQI)? Don't see it anywhere, but wanted to see if anyone else knew of anything. Many thanks -- View this message in context: http://n4.nabble.com/AHRQ-Patient-Quality-Indicators-tp1747243p1747243.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] lattice: how to add points to the plot generated by levelplot()?
I am using levelplot() function from pkg:lattice and I want to add some
points
to the plot generated by levelplot()
similarly as in basic R graphic sequence: plot(...); points(...),
but it does not work.
I was reading documentation for lattice, but so far without much
success.
I would very much appreciate some tips.
Best regards,
Ryszard
--
Confidentiality Notice: This message is private and may ...{{dropped:11}}
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Re: [R] Problem comparing hazard ratios
Ravi Varadhan wrote:
Frank,
Is there an article that discusses this idea of bootstrapping the ranks of
the likelihood ratio chi-square
Statistics to assess relative importance of predictors in time-to-event data
(specifically Cox PH model)?
Thanks,
Ravi.
Do require(rms); ?anova.rms and see related articles:
@Article{hal09usi,
author = {Hall, Peter and Miller, Hugh},
title = {Using the bootstrap to quantify the authority of an
empirical ranking},
journal = Annals of Stat,
year = 2009,
volume = 37,
number = {6B},
pages ={3929-3959},
annote = {confidence interval for ranks;genomics;high
dimension;independent component bootstrap;$m$-out-of-$n$
bootstrap;ordering;overlap interval;prediction interval;synchronous
bootstrap;ordinary bootstrap may not provide accurate confidence
intervals for ranks;may need a different bootstrap if the number of
parameters being ranked increases with $n$ or is large;estimating $m$ is
difficult;in their first example, where $m=0.355n$, the ordinary
bootstrap provided a lower bound to the lengths of more accurate
confidence intervals of ranks}
}
@Article{xie09con,
author = {Xie, Minge and Singh, Kesar and Zhang, {Cun-Hui}},
title = {Confidence intervals for population ranks in the presence
of ties and near ties},
journal = JASA,
year = 2009,
volume = 104,
number = 486,
pages ={775-787},
annote = {bootstrap ranks;ranking;nonstandard bootstrap
inference;rank inference;slow convergence rate;smooth ranks in the
presence of near ties;rank inference for fixed effects risk adjustment
models}
}
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Frank E Harrell Jr
Sent: Tuesday, March 30, 2010 3:57 PM
To: Michal Figurski
Cc: r-help@r-project.org
Subject: Re: [R] Problem comparing hazard ratios
Michal Figurski wrote:
Dear R-Helpers,
I am a novice in survival analysis. I have the following code:
for (i in 3:12) print(coxph(Surv(time, status)~a[,i], data=a))
I used it to fit the Cox Proportional Hazard models separately for every
available parameter (columns 3:12) in my data set - with intention to
compare the Hazard Ratios.
However, some of my variables are in range 0.1 to 1.6, others in range
5000 to 9000. How do I compare HRs between such variables?
I have rescaled all the variables to be in 0 to 1 range - is this the
proper way to go? Is there a way to somehow calculate the same HRs (as
for rescaled parameters) from the HRs for original parameters?
Many thanks in advance.
There are a lot of issues related to this that will require a good bit
of study, both in survival analysis and in regression. I would start
with bootstrapping the ranks of the likelihood ratio chi-square
statistics of the competing biomarkers.
Frank
--
Frank E Harrell Jr Professor and ChairmanSchool of Medicine
Department of Biostatistics Vanderbilt University
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[R] ODD and EVEN numbers
Hi, anyone here who knows how to determine if an integer is odd or even in R? Thanks. tj -- View this message in context: http://n4.nabble.com/ODD-and-EVEN-numbers-tp1747032p1747032.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] You are right and the problem is solved. Re: about the possible errors in Rgraphviz Package
Hi Gabor, I just used your R code below and the code worked properly without any error messages. Attached is the output graph, which may be the one you expected. library(Rgraphviz) set.seed(123) V - letters[1:10] M - 1:4 g1 - randomGraph(V, M, 0.2) g1 plot(g1) Thanks. Howard On Wed Mar 31 11:18:25 EDT 2010, Gabor Grothendieck ggrothendi...@gmail.com wrote: By the way, just in case you did not read the entire message R crashed when I tried to run the code from the vignette. On Wed, Mar 31, 2010 at 10:52 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: Based on your success I thought I would try again. I am not sure why I had more success this time but this time I got this far even though I did not change my path at all or make any system changes from what I had before. ??I did reinstall Rgraphviz but used the previously installed graphviz. ?? I tried this code taken from the Rgrpahviz vignette: library(Rgraphviz) Loading required package: graph Loading required package: grid set.seed(123) V - letters[1:10] M - 1:4 g1 - randomGraph(V, M, 0.2) g1 A graphNEL graph with undirected edges Number of Nodes = 10 Number of Edges = 16 but when I tried to plot it R crashed. plot(g1) It did produce this message on the Windows console (not the R console): Error: Layout type: dot not recognized. Use one of: There was nothing after the of: R.version.string [1] R version 2.10.1 Patched (2010-03-10 r51276) win.version() [1] Windows Vista (build 6002) Service Pack 2 packageDescription(Rgraphviz)$Version [1] 1.24.0 graphvizVersion() $installed_version [1] ?2.20.3? $build_version [1] ?2.20.3? On Wed, Mar 31, 2010 at 9:56 AM, HU,ZHENGJUN h...@ufl.edu wrote: Hi Martin, ??It is really a 'PATH' problem. After adding C:\Program Files\Graphviz2.20\bin to the 'PATH' environment variable, the Rgraphviz package can be loaded without any error messages. ??Sorry that I ONLY set my 'PATH' environment variable correctly for R but not for Graphviz. ??Thank you and Duncan so much for your great help. ??Howard On Tue Mar 30 18:12:54 EDT 2010, Martin Morgan mtmor...@fhcrc.org wrote: On 03/30/2010 03:06 PM, HU,ZHENGJUN wrote: Hi Martin, ??I am 100% sure that I set my 'PATH' environment variable correctly because all other packages can loaded correctly as well as because R can be run correctly under both MS DOS and MS Windows XP. Also, I can create some simple R packages correctly. The PATH must be set correctly to include graphviz, as in my example below. Copy and paste the output of ??strsplit(Sys.getenv(PATH), ;) and ??list.files(strsplit(Sys.getenv(PATH), ;)[[1]][[14]], dll) Martin ??Thanks. ??Howard On Tue Mar 30 16:58:55 EDT 2010, Martin Morgan mtmor...@fhcrc.org wrote: On 03/30/2010 01:13 PM, HU,ZHENGJUN wrote: Hi Martin, ??I uninstalled graphviz-2.26.3.msi and then installed graphviz-2.20.3.1.msi. Then installed the Rgraphviz package again. As expected, I got the same error messages as before: Error in inDL(x, as.logical(local), as.logical(now), ...) : ??unable to load shared library 'C:/PROGRA~1/R/R-210~1.1/library/Rgraphviz/libs/Rgraphviz.dll': ??LoadLibrary failure: ??The specified module could not be found. 'LoadLibrary' is being vague, the 'specified modules' are the DLLs from graphviz. Have you checked that your 'PATH' environment variable is set correctly? In R ?? strsplit(Sys.getenv(PATH), ;) $PATH ??... ??[14] C:\\Program Files\\Graphviz2.20\\bin ... The relevant files in this directory might look like list.files(strsplit(Sys.getenv(PATH), ;)[[1]][[14]], dll) ??[1] iconv.dll ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ??intl.dll ??[3] jpeg62.dll ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? libcairo-2.dll ??[5] libcdt-4.dll ?? ?? ?? ?? ?? ?? ?? ?? ?? libcgraph-4.dll ??[7] libexpat.dll ?? ?? ?? ?? ?? ?? ?? ?? ?? libfontconfig-1.dll ??[9] libfreetype-6.dll ?? ?? ?? ?? ?? ?? ??libgdk_pixbuf-2.0-0.dll [11] libglib-2.0-0.dll ?? ?? ?? ?? ?? ?? ??libgmodule-2.0-0.dll [13] libgobject-2.0-0.dll ?? ?? ?? ?? ?? libgraph-4.dll [15] libgvc-4.dll ?? ?? ?? ?? ?? ?? ?? ?? ?? libgvplugin_core-5.dll [17] libgvplugin_dot_layout-5.dll ?? libgvplugin_gd-5.dll [19] libgvplugin_neato_layout-5.dll libgvplugin_pango-5.dll [21] libltdl-3.dll ?? ?? ?? ?? ?? ?? ?? ?? ??libpango-1.0-0.dll [23] libpangocairo-1.0-0.dll ?? ?? ?? ??libpangoft2-1.0-0.dll [25] libpangowin32-1.0-0.dll ?? ??
[R] change mbmdr odds ratio
I am using the package 'mbmdr' based on the model-base multifactor dimensionality reduction method by Calle et al. In the paper, mbmdr is used for a case-control study. My data is not case-control, i.e. I have a lot more controls than cases. Does anyone know if the odds ratio in the fuction mbmdr is automatically set to 1 OR is it default to the odds of disease based on the input data OR can it be user defined? Perhaps I am just blind or too novice of an R user, but I do not see where that can be specified in the mbmdr help file. Thanks in advance! -- View this message in context: http://n4.nabble.com/change-mbmdr-odds-ratio-tp1747022p1747022.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] You are right and the problem is solved. Re: about the possible errors in Rgraphviz Package
Hi Martin, It is really a 'PATH' problem. After adding C:\Program Files\Graphviz2.20\bin to the 'PATH' environment variable, the Rgraphviz package can be loaded without any error messages. Sorry that I ONLY set my 'PATH' environment variable correctly for R but not for Graphviz. Thank you and Duncan so much for your great help. Howard On Tue Mar 30 18:12:54 EDT 2010, Martin Morgan mtmor...@fhcrc.org wrote: On 03/30/2010 03:06 PM, HU,ZHENGJUN wrote: Hi Martin, I am 100% sure that I set my 'PATH' environment variable correctly because all other packages can loaded correctly as well as because R can be run correctly under both MS DOS and MS Windows XP. Also, I can create some simple R packages correctly. The PATH must be set correctly to include graphviz, as in my example below. Copy and paste the output of strsplit(Sys.getenv(PATH), ;) and list.files(strsplit(Sys.getenv(PATH), ;)[[1]][[14]], dll) Martin Thanks. Howard On Tue Mar 30 16:58:55 EDT 2010, Martin Morgan mtmor...@fhcrc.org wrote: On 03/30/2010 01:13 PM, HU,ZHENGJUN wrote: Hi Martin, I uninstalled graphviz-2.26.3.msi and then installed graphviz-2.20.3.1.msi. Then installed the Rgraphviz package again. As expected, I got the same error messages as before: Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/R-210~1.1/library/Rgraphviz/libs/Rgraphviz.dll': LoadLibrary failure: The specified module could not be found. 'LoadLibrary' is being vague, the 'specified modules' are the DLLs from graphviz. Have you checked that your 'PATH' environment variable is set correctly? In R strsplit(Sys.getenv(PATH), ;) $PATH ... [14] C:\\Program Files\\Graphviz2.20\\bin ... The relevant files in this directory might look like list.files(strsplit(Sys.getenv(PATH), ;)[[1]][[14]], dll) [1] iconv.dll intl.dll [3] jpeg62.dll libcairo-2.dll [5] libcdt-4.dll libcgraph-4.dll [7] libexpat.dll libfontconfig-1.dll [9] libfreetype-6.dll libgdk_pixbuf-2.0-0.dll [11] libglib-2.0-0.dll libgmodule-2.0-0.dll [13] libgobject-2.0-0.dll libgraph-4.dll [15] libgvc-4.dll libgvplugin_core-5.dll [17] libgvplugin_dot_layout-5.dll libgvplugin_gd-5.dll [19] libgvplugin_neato_layout-5.dll libgvplugin_pango-5.dll [21] libltdl-3.dll libpango-1.0-0.dll [23] libpangocairo-1.0-0.dlllibpangoft2-1.0-0.dll [25] libpangowin32-1.0-0.dlllibpathplan-4.dll [27] libpng12.dll libxml2.dll Martin Thank you. Howard On Tue Mar 30 15:36:05 EDT 2010, Martin Morgan mtmor...@fhcrc.org wrote: On 03/30/2010 10:24 AM, HU,ZHENGJUN wrote: Hi Duncan, (They are pretty hard to find, but I think you can find them on the Bioconductor site.) It is not enough to install the Rgraphviz package, you also need to install Graphviz. Yes I did. Before installing the Rgraphviz package successfully, (1) I downloaded graphviz-2.26.3.msi for MS Windows (XP) and installed it successfully and (2) I also installed the packages from Bioconductor by: (Note: I use MS Windows XP and R 2.10.1 version) This is a bioconductor package so please ask on the Bioconductor mailing list http://bioconductor.org/docs/mailList.html See the 'README' file in the 'tar.gz' file at http://bioconductor.org/packages/release/Software.html http://bioconductor.org/packages/2.5/bioc/html/Rgraphviz.html http://bioconductor.org/packages/2.5/bioc/src/contrib/Rgraphviz_1.24.0.tar.gz which says o. install Graphviz ***2.20.3.1*** Windows ***binary*** distribution from http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.1.msi you must use this version of graphviz. File paths must be correct. Martin source(http://www.bioconductor.org/biocLite.R;) biocLite() I got those error messages: Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/R-210~1.1/library/Rgraphviz/libs/Rgraphviz.dll': LoadLibrary failure: The specified module could not be found. Obviously, it seems it is the package problem because it should go to 'C:/PROGRA~1/R/R-2.10.1/library/Rgraphviz/libs/Rgraphviz.dll' instead of 'C:/PROGRA~1/R/R-210~1.1/library/Rgraphviz/libs/Rgraphviz.dll' Thank you for the reply. Howard On Tue Mar 30 12:50:44 EDT 2010, Duncan Murdoch murd...@stats.uwo.ca wrote: On 30/03/2010 10:44 AM, HU,ZHENGJUN wrote: Hi All, I tried to install the package of Rgraphviz in the following two ways successfully: source(http://bioconductor.org/biocLite.R;) biocLite(Rgraphviz) install.packages(pkgs=C:/Progra~1/R/lib_download/Rgraphviz_1.24.0.zip, lib=C:/Progra~1/R/R-2.10.1/library, repos=NULL) but when I loaded the package though library(Rgraphviz) or library(Rgraphviz), and got the same error message below: Error in inDL(x, as.logical(local),
[R] How to work with the result of JRip?
Hello, I want to work with the result of JRip, but I don't know how to access it. I produce a rule like below: rule = JRip(Cls ~., data=dd) The result is: JRIP rules: === (C7 = 1) = Cls=TRUE (384.0/0.0) = Cls=FALSE (1344.0/0.0) \par Number of Rules : 2 I want to work with the above rule..for instance I need the number of rules, the number of Attribute Tests. But I don't know how to receive it. Do anyone know how we can get it? I would be glad for the reply. Thanks, -- View this message in context: http://n4.nabble.com/How-to-work-with-the-result-of-JRip-tp1746858p1746858.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Summing data based on certain conditions
Dear all, I have a dataset of 1073 rows, the first 15 which look as follows: data[1:15,] date year month day rammday thmmday 1 3/8/1988 1988 3 8 1.43 0.94 2 3/15/1988 1988 3 15 2.86 0.66 3 3/22/1988 1988 3 22 5.06 3.43 4 3/29/1988 1988 3 29 18.76 10.93 5 4/5/1988 1988 4 5 4.49 2.70 6 4/12/1988 1988 4 12 8.57 4.59 7 4/16/1988 1988 4 16 31.18 22.18 8 4/19/1988 1988 4 19 19.67 12.33 9 4/26/1988 1988 4 26 3.14 1.79 10 5/3/1988 1988 5 3 11.51 6.33 11 5/10/1988 1988 5 10 5.64 2.89 12 5/17/1988 1988 5 17 37.46 20.89 13 5/24/1988 1988 5 24 9.86 9.81 14 5/31/1988 1988 5 31 13.00 8.63 15 6/7/1988 1988 6 7 0.43 0.00 I am looking for a way by which I can create monthly totals of rammday (rainfall in mm/day; column 5) by doing the following: For each case where the month value and the year are the same (e.g. 3 and 1988, in the first four rows), find the mean of the the corresponding rammday values and then times by the number of days in that month (i.e. 31 in this case). Note however that the number of month values in each case isn't always the same (e.g. in this subset of data, there are 4 values for month 3, 5 for month 4 and 5 for month 5). Also the months will of course recycle for the following years, so it's not simply a case of finding a monthly total for *all* the 3s in the whole dataset, just those associated with each year in turn. How would I go about doing this in R? Any help will be gratefully received. Many thanks, Steve _ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] You are right and the problem is solved. Re: about the possible errors in Rgraphviz Package
On 03/31/2010 11:44 AM, Gabor Grothendieck wrote: I got an error message *AND* R becomes unusable and had to be restarted. Using dependency walker it seems to be complaining about R.dll so I copied all of my ...\R\bin\R*.dll files to .. ...\win-library\2.10\Rgraphviz\libs. Then it complained about IESHIMS.dll so I copied \Program Files\Internet Explorer\IESHIMS.dll to ...\win-library\2.10\Rgraphviz\libs. Looking at dependency walker these DLLs: LIBCDT-4.DLL, LIBGRAPH-4.DLL, and LIBGVC-4.DLL all seem to point to correct place. I still have this message in dependency walker: Warning: At least one module has an unresolved import due to a missing export function in a delay-load dependent module. There is a red mark beside: c:\windows\system32\IEFRAME.DLL but its not missing. I also tried reinstalling R using the latest R 2.10.1. I am still getting the same result, namely I can run the indicated code up to but not including plot(g1) but if I run plot(g1) R crashes and must be restarted. Wow, I didn't mean to put you through such convolutions, and am sorry that I can't offer an immediate solution. Martin On Wed, Mar 31, 2010 at 12:54 PM, Martin Morgan mtmor...@fhcrc.org wrote: On 03/31/2010 08:18 AM, Gabor Grothendieck wrote: By the way, just in case you did not read the entire message R crashed I think you mean that you got an error message, not that R became unusable? More below... when I tried to run the code from the vignette. On Wed, Mar 31, 2010 at 10:52 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: Based on your success I thought I would try again. I am not sure why I had more success this time but this time I got this far even though I did not change my path at all or make any system changes from what I had before. I did reinstall Rgraphviz but used the previously installed graphviz. I tried this code taken from the Rgrpahviz vignette: library(Rgraphviz) Loading required package: graph Loading required package: grid set.seed(123) V - letters[1:10] M - 1:4 g1 - randomGraph(V, M, 0.2) g1 A graphNEL graph with undirected edges Number of Nodes = 10 Number of Edges = 16 but when I tried to plot it R crashed. plot(g1) It did produce this message on the Windows console (not the R console): Error: Layout type: dot not recognized. Use one of: In the past this has come about when accessing incorrect graphviz DLLs. The gory detail (if I remember correctly) is that a FILE* gets allocated in Rgraphviz and passed to graphviz, and if there is a compiler mismatch then there are no guarantees about FILE* representation. The implication is that your Rgraphviz and graphiz are at least partly out of sync, but it could also be that I am 'getting lucky'. When you say (quoting from above)... did not change my path at all or make any system changes from what I the implication is that your PATH was already set to include a graphviz2.20\\bin directory; I'd encourage you to confirm that. Yes, My path is: PATH=C:\Graphviz2.20\bin;...more stuff... And recognizing that you might justifiably be willing to put this on the shelf, you might also use Dependency Walker (http://www.dependencywalker.com/) to open the Rgraphviz DLL (R_HOME/libraries/Rgraphviz/libs/Rgraphviz.dll), right click on the RGRAPHVIZ.DLL showing up in the top left panel, and choose 'Full paths', and verify that LIBCDT-4.DLL, LIBGRAPH-4.DLL, and LIBGVC-4.DLL all point to Graphviz2.20\bin. Martin There was nothing after the of: R.version.string [1] R version 2.10.1 Patched (2010-03-10 r51276) win.version() [1] Windows Vista (build 6002) Service Pack 2 packageDescription(Rgraphviz)$Version [1] 1.24.0 graphvizVersion() $installed_version [1] ‘2.20.3’ $build_version [1] ‘2.20.3’ On Wed, Mar 31, 2010 at 9:56 AM, HU,ZHENGJUN h...@ufl.edu wrote: Hi Martin, It is really a 'PATH' problem. After adding C:\Program Files\Graphviz2.20\bin to the 'PATH' environment variable, the Rgraphviz package can be loaded without any error messages. Sorry that I ONLY set my 'PATH' environment variable correctly for R but not for Graphviz. Thank you and Duncan so much for your great help. Howard On Tue Mar 30 18:12:54 EDT 2010, Martin Morgan mtmor...@fhcrc.org wrote: On 03/30/2010 03:06 PM, HU,ZHENGJUN wrote: Hi Martin, I am 100% sure that I set my 'PATH' environment variable correctly because all other packages can loaded correctly as well as because R can be run correctly under both MS DOS and MS Windows XP. Also, I can create some simple R packages correctly. The PATH must be set correctly to include graphviz, as in my example below. Copy and paste the output of strsplit(Sys.getenv(PATH), ;) and list.files(strsplit(Sys.getenv(PATH), ;)[[1]][[14]], dll) Martin Thanks. Howard On Tue Mar 30 16:58:55 EDT 2010, Martin Morgan mtmor...@fhcrc.org wrote: On 03/30/2010 01:13 PM, HU,ZHENGJUN wrote: Hi
Re: [R] ODD and EVEN numbers
See %% under ?Arithmetic tj wrote: Hi, anyone here who knows how to determine if an integer is odd or even in R? Thanks. tj __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lattice: how to add points to the plot generated by levelplot()?
Czerminski, Ryszard wrote:
I am using levelplot() function from pkg:lattice and I want to add some
points
to the plot generated by levelplot()
It's best to include a small example of what you have done so far, and
what you want to further do. Actual R code with a small sample dataset
is great.
similarly as in basic R graphic sequence: plot(...); points(...),
but it does not work.
I was reading documentation for lattice, but so far without much
success.
I would very much appreciate some tips.
Most base graphics functions like point have a grid equivalent. In this
case, use grid.points.
levelplot(runif(100)~runif(100)*runif(100),
panel = function(...) {
panel.levelplot(...)
grid.points(.1, .1, pch = 2)
})
I found the Lattice book and the R Graphics book invaluable, both are
worth getting.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] ODD and EVEN numbers
On Mar 31, 2010, at 12:43 PM, tj wrote:
Hi,
anyone here who knows how to determine if an integer is odd or
even in
R?
Thanks.
2 %% 2 == 0
[1] TRUE
3 %% 2 == 0
[1] FALSE
is.even - function(x){ x %% 2 == 0 }
is.even(2)
[1] TRUE
--
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Summing data based on certain conditions
?ave or ?tapply Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Steve Murray Sent: Wednesday, March 31, 2010 10:20 AM To: r-help@r-project.org Subject: [R] Summing data based on certain conditions Dear all, I have a dataset of 1073 rows, the first 15 which look as follows: data[1:15,] date year month day rammday thmmday 1 3/8/1988 1988 3 8 1.43 0.94 2 3/15/1988 1988 3 15 2.86 0.66 3 3/22/1988 1988 3 22 5.06 3.43 4 3/29/1988 1988 3 29 18.76 10.93 5 4/5/1988 1988 4 5 4.49 2.70 6 4/12/1988 1988 4 12 8.57 4.59 7 4/16/1988 1988 4 16 31.18 22.18 8 4/19/1988 1988 4 19 19.67 12.33 9 4/26/1988 1988 4 26 3.14 1.79 10 5/3/1988 1988 5 3 11.51 6.33 11 5/10/1988 1988 5 10 5.64 2.89 12 5/17/1988 1988 5 17 37.46 20.89 13 5/24/1988 1988 5 24 9.86 9.81 14 5/31/1988 1988 5 31 13.00 8.63 15 6/7/1988 1988 6 7 0.43 0.00 I am looking for a way by which I can create monthly totals of rammday (rainfall in mm/day; column 5) by doing the following: For each case where the month value and the year are the same (e.g. 3 and 1988, in the first four rows), find the mean of the the corresponding rammday values and then times by the number of days in that month (i.e. 31 in this case). Note however that the number of month values in each case isn't always the same (e.g. in this subset of data, there are 4 values for month 3, 5 for month 4 and 5 for month 5). Also the months will of course recycle for the following years, so it's not simply a case of finding a monthly total for *all* the 3s in the whole dataset, just those associated with each year in turn. How would I go about doing this in R? Any help will be gratefully received. Many thanks, Steve _ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] strip.custom with strip on left for three conditioning variables
I want to use a strip.custom as with useOuterStrips for three conditioning variables. useOuterStrips restricts this to only two conditioning variables, and I cannot figure out how to write strip.custom properly to do this. library(lattice) mtcars$HP - equal.count(mtcars$hp) #with two factors x2-xyplot(mpg ~ disp | HP + factor(cyl), mtcars) useOuterStrips(x2) #with three factors x3-xyplot(mpg ~ disp | HP + factor(cyl) + factor(carb), mtcars) update(x3,strip=strip.custom(which.given= 1), strip2=strip.custom(which.given= 2), strip.left=strip.custom(which.given=3) ) -- Patrick Schmitz Graduate Student Plant Biology 1206 West Gregory Drive RM 1500 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ODD and EVEN numbers
(foo %% 2) == 0 See ?%% HTH Stephan tj schrieb: Hi, anyone here who knows how to determine if an integer is odd or even in R? Thanks. tj __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lattice: how to add points to the plot generated bylevelplot()?
Tip 1: This sort of thing is done with panel functions. ?xyplot and
?panel.xyplot is where to start.
Tip 2: grid functions are generally not necessary, as translations of the
common ones are part of lattice. See ?panel.points
Tip 3: Deepayan's book provides a gentler explanation of these matters with
more examples than R's man pages.
Tip 4: Depending on your needs and predilections, you may prefer to use
ggplot2.
Bert Gunter
Genentech Nonclinical Biostatistics
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Erik Iverson
Sent: Wednesday, March 31, 2010 12:54 PM
To: Czerminski, Ryszard
Cc: R-help@r-project.org
Subject: Re: [R] lattice: how to add points to the plot generated
bylevelplot()?
Czerminski, Ryszard wrote:
I am using levelplot() function from pkg:lattice and I want to add some
points
to the plot generated by levelplot()
It's best to include a small example of what you have done so far, and
what you want to further do. Actual R code with a small sample dataset
is great.
similarly as in basic R graphic sequence: plot(...); points(...),
but it does not work.
I was reading documentation for lattice, but so far without much
success.
I would very much appreciate some tips.
Most base graphics functions like point have a grid equivalent. In this
case, use grid.points.
levelplot(runif(100)~runif(100)*runif(100),
panel = function(...) {
panel.levelplot(...)
grid.points(.1, .1, pch = 2)
})
I found the Lattice book and the R Graphics book invaluable, both are
worth getting.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
